{ "cells": [ { "cell_type": "markdown", "id": "e5c34bf1", "metadata": { "colab_type": "text", "id": "view-in-github" }, "source": [ "\"Open \n", "\"Open " ] }, { "cell_type": "markdown", "id": "1b937be1", "metadata": {}, "source": [ "## Freesurefer Example\n", "\n", "Author: Steffen Bollmann" ] }, { "cell_type": "markdown", "id": "7hrfYzlFU6pN", "metadata": { "id": "7hrfYzlFU6pN" }, "source": [ "## Setup Neurodesk" ] }, { "cell_type": "code", "execution_count": 1, "id": "DwyOSXw4U3Kn", "metadata": { "colab": { "base_uri": "https://localhost:8080/" }, "id": "DwyOSXw4U3Kn", "outputId": "9596fece-8f39-4b8a-b188-b9af0d12fdcd" }, "outputs": [], "source": [ "import os\n", "import sys\n", "IN_COLAB = 'google.colab' in sys.modules\n", "\n", "if IN_COLAB:\n", " os.environ[\"LD_PRELOAD\"] = \"\";\n", " os.environ[\"APPTAINER_BINDPATH\"] = \"/content,/tmp,/cvmfs\"\n", " os.environ[\"MPLCONFIGDIR\"] = \"/content/matplotlib-mpldir\"\n", " os.environ[\"LMOD_CMD\"] = \"/usr/share/lmod/lmod/libexec/lmod\"\n", "\n", " !curl -J -O https://raw.githubusercontent.com/NeuroDesk/neurocommand/main/googlecolab_setup.sh\n", " !chmod +x googlecolab_setup.sh\n", " !./googlecolab_setup.sh\n", "\n", " os.environ[\"MODULEPATH\"] = ':'.join(map(str, list(map(lambda x: os.path.join(os.path.abspath('/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/'), x),os.listdir('/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/')))))\n", "\n", " from google.colab import output\n", " output.enable_custom_widget_manager()\n", " !pip install ipyniivue" ] }, { "cell_type": "code", "execution_count": 2, "id": "7dc1211f-1450-4d97-b35f-3d93d5865d57", "metadata": { "tags": [] }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "vendor_id\t: AuthenticAMD\n", "model name\t: AMD EPYC 7742 64-Core Processor\n" ] } ], "source": [ "# Output CPU information:\n", "!cat /proc/cpuinfo | grep 'vendor' | uniq\n", "!cat /proc/cpuinfo | grep 'model name' | uniq" ] }, { "cell_type": "code", "execution_count": 1, "id": "00345266-eb39-40c9-a29a-32cda10ebba3", "metadata": { "colab": { "base_uri": "https://localhost:8080/" }, "id": "00345266-eb39-40c9-a29a-32cda10ebba3", "outputId": "86874c10-4735-471f-e569-23a6c9f944df" }, "outputs": [ { "data": { "text/plain": [ "['freesurfer/7.3.2']" ] }, "execution_count": 1, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# we can use lmod to load fsl in a specific version\n", "import lmod\n", "await lmod.load('freesurfer/7.3.2')\n", "await lmod.list()" ] }, { "cell_type": "code", "execution_count": 2, "id": "2e447e8b-a6fd-4365-9da3-3de21a4654b2", "metadata": { "colab": { "base_uri": "https://localhost:8080/" }, "id": "2e447e8b-a6fd-4365-9da3-3de21a4654b2", "outputId": "d5667809-043f-408a-9d46-bbc291775cc2" }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n", "USAGE: recon-all\n", "\n", " Required Arguments:\n", " -subjid \n", " -\n", "\n", " Fully-Automated Directive:\n", " -all : performs all stages of cortical reconstruction\n", " -autorecon-all : same as -all\n", "\n", " Manual-Intervention Workflow Directives:\n", " -autorecon1 : process stages 1-5 (see below)\n", " -autorecon2 : process stages 6-23\n", " after autorecon2, check white surfaces:\n", " a. if wm edit was required, then run -autorecon2-wm\n", " b. if control points added, then run -autorecon2-cp\n", " c. proceed to run -autorecon3\n", " -autorecon2-cp : process stages 12-23 (uses -f w/ mri_normalize, -keep w/ mri_seg)\n", " -autorecon2-wm : process stages 15-23\n", " -autorecon2-inflate1 : 6-18\n", " -autorecon2-perhemi : tess, sm1, inf1, q, fix, sm2, inf2, finalsurf, ribbon\n", " -autorecon3 : process stages 24-34\n", " if edits made to correct pial, then run -autorecon-pial\n", " -hemi ?h : just do lh or rh (default is to do both)\n", "\n", " Autorecon Processing Stages (see -autorecon# flags above):\n", " 1. Motion Correction and Conform\n", " 2. NU (Non-Uniform intensity normalization)\n", " 3. Talairach transform computation\n", " 4. Intensity Normalization 1\n", " 5. Skull Strip\n", "\n", " 6. EM Register (linear volumetric registration)\n", " 7. CA Intensity Normalization\n", " 8. CA Non-linear Volumetric Registration \n", " 9. Remove neck\n", " 10. EM Register, with skull\n", " 11. CA Label (Aseg: Volumetric Labeling) and Statistics\n", "\n", " 12. Intensity Normalization 2 (start here for control points)\n", " 13. White matter segmentation\n", " 14. Edit WM With ASeg\n", " 15. Fill (start here for wm edits)\n", " 16. Tessellation (begins per-hemisphere operations)\n", " 17. Smooth1\n", " 18. Inflate1\n", " 19. QSphere\n", " 20. Automatic Topology Fixer\n", " 21. White Surfs (start here for brain edits for pial surf)\n", " 22. Smooth2\n", " 23. Inflate2\n", "\n", " 24. Spherical Mapping\n", " 25. Spherical Registration \n", " 26. Spherical Registration, Contralater hemisphere\n", " 27. Map average curvature to subject\n", " 28. Cortical Parcellation (Labeling)\n", " 29. Cortical Parcellation Statistics\n", " 30. Pial Surfs\n", " 31. WM/GM Contrast\n", " 32. Cortical Ribbon Mask\n", " 33. Cortical Parcellation mapped to ASeg\n", " 34 Brodmann and exvio EC labels\n", "\n", " Step-wise Directives\n", " See -help\n", "\n", " Expert Preferences\n", " -pons-crs C R S : col, row, slice of seed point for pons, used in fill\n", " -cc-crs C R S : col, row, slice of seed point for corpus callosum, used in fill\n", " -lh-crs C R S : col, row, slice of seed point for left hemisphere, used in fill\n", " -rh-crs C R S : col, row, slice of seed point for right hemisphere, used in fill\n", " -nofill : do not use the automatic subcort seg to fill\n", " -watershed cmd : control skull stripping/watershed program\n", " -xmask file : custom external brain mask to replace automated skullstripping\n", " -wsless : decrease watershed threshold (leaves less skull, but can strip more brain)\n", " -wsmore : increase watershed threshold (leaves more skull, but can strip less brain)\n", " -wsatlas : use atlas when skull stripping\n", " -no-wsatlas : do not use atlas when skull stripping\n", " -no-wsgcaatlas : do not use GCA atlas when skull stripping\n", " -wsthresh pct : explicity set watershed threshold\n", " -wsseed C R S : identify an index (C, R, S) point in the skull\n", " -norm3diters niters : number of 3d iterations for mri_normalize\n", " -normmaxgrad maxgrad : max grad (-g) for mri_normalize. Default is 1.\n", " -norm1-b N : in the _first_ usage of mri_normalize, use control \n", " point with intensity N below target (default=10.0) \n", " -norm2-b N : in the _second_ usage of mri_normalize, use control \n", " point with intensity N below target (default=10.0) \n", " -norm1-n N : in the _first_ usage of mri_normalize, do N number \n", " of iterations\n", " -norm2-n N : in the _second_ usage of mri_normalize, do N number \n", " of iterations\n", " -cm : conform volumes to the min voxel size \n", " -no-fix-with-ga : do not use genetic algorithm when fixing topology\n", " -fix-diag-only : topology fixer runs until ?h.defect_labels files\n", " are created, then stops\n", " -seg-wlo wlo : set wlo value for mri_segment and mris_make_surfaces\n", " -seg-ghi ghi : set ghi value for mri_segment and mris_make_surfaces\n", " -nothicken : pass '-thicken 0' to mri_segment\n", " -no-ca-align-after : turn off -align-after with mri_ca_register\n", " -no-ca-align : turn off -align with mri_ca_label\n", " -deface : deface subject, written to orig_defaced.mgz\n", "\n", " -expert file : read-in expert options file\n", " -xopts-use : use pre-existing expert options file\n", " -xopts-clean : delete pre-existing expert options file\n", " -xopts-overwrite : overwrite pre-existing expert options file\n", " -termscript script : run script before exiting (multiple -termscript flags possible)\n", " This can be good for running custom post-processing after recon-all\n", " The script must be in your path. The subjid is passed as the only argument\n", " The current directory is changed to SUBJECTS_DIR before the script is run\n", " The script should exit with 0 unless there is an error\n", "\n", " -mprage : assume scan parameters are MGH MP-RAGE protocol\n", " -washu_mprage : assume scan parameters are Wash.U. MP-RAGE protocol.\n", " both mprage flags affect mri_normalize and mri_segment,\n", " and assumes a darker gm.\n", " -schwartzya3t-atlas : for tal reg, use special young adult 3T atlas\n", "\n", " -threads num : set number of threads to use\n", "\n", " Notification Files (Optional)\n", " -waitfor file : wait for file to appear before beginning\n", " -notify file : create this file after finishing\n", "\n", " Status and Log files (Optional)\n", " -log file : default is scripts/recon-all.log\n", " -status file : default is scripts/recon-all-status.log\n", " -noappend : start new log and status files instead of appending\n", " -no-isrunning : do not check whether this subject is currently being processed\n", "\n", " Segmentation of substructures of hippocampus and brainstem \n", " (These deprecated; please see segmentHA_T1.sh, segmentHA_T1.sh, segmentHA_T1_long.sh, segmentBS.sh)\n", " -hippocampal-subfields-T1 : segmentation of hippocampal subfields using input T1 scan\n", " -hippocampal-subfields-T2 file ID : segmentation using an additional scan (given by file);\n", " ID is a user-defined identifier for the analysis\n", " -hippocampal-subfields-T1T2 file ID : segmentation using additional scan (given by file) and input T1\n", " simultaneously; ID is a user-defined identifier for the analysis\n", " -brainstem-structures : segmentation of brainstem structures\n", "\n", " Other Arguments (Optional)\n", " -sd subjectsdir : specify subjects dir (default env SUBJECTS_DIR)\n", " -mail username : mail user when done\n", " -umask umask : set unix file permission mask (default 002)\n", " -grp groupid : check that current group is alpha groupid \n", " -onlyversions : print version of each binary and exit\n", " -debug : print out lots of info\n", " -allowcoredump : set coredump limit to unlimited\n", " -dontrun : do everything but execute each command\n", " -version : print version of this script and exit\n", " -help : voluminous bits of wisdom\n", "\n" ] } ], "source": [ "!recon-all" ] }, { "cell_type": "markdown", "id": "11961012-a84e-40d5-a2df-086ede86d163", "metadata": { "id": "11961012-a84e-40d5-a2df-086ede86d163" }, "source": [ "## download data" ] }, { "cell_type": "code", "execution_count": 3, "id": "b2513194-a19e-43e5-80a8-9dccc4d47bb9", "metadata": { "colab": { "base_uri": "https://localhost:8080/" }, "id": "b2513194-a19e-43e5-80a8-9dccc4d47bb9", "outputId": "57372e2a-1225-4c7b-e6c4-548fe1852411" }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "--2023-06-29 01:43:20-- https://imaging.org.au/uploads/Human7T/mp2rageModel_L13_work03-plus-hippocampus-7T-sym-norm-mincanon_v0.8.nii\n", "Resolving imaging.org.au (imaging.org.au)... 203.101.229.7\n", "Connecting to imaging.org.au (imaging.org.au)|203.101.229.7|:443... connected.\n", "HTTP request sent, awaiting response... 200 OK\n", "Length: 1536000352 (1.4G) [application/octet-stream]\n", "Saving to: ‘./mp2rage.nii’\n", "\n", "./mp2rage.nii 100%[===================>] 1.43G 20.4MB/s in 74s \n", "\n", "2023-06-29 01:44:35 (19.8 MB/s) - ‘./mp2rage.nii’ saved [1536000352/1536000352]\n", "\n" ] } ], "source": [ "![ -f ./mp2rage.nii ] && echo \"$FILE exist.\" || wget https://imaging.org.au/uploads/Human7T/mp2rageModel_L13_work03-plus-hippocampus-7T-sym-norm-mincanon_v0.8.nii -O ./mp2rage.nii " ] }, { "cell_type": "code", "execution_count": 4, "id": "37f99b61-55a6-4016-a697-bf065a083c7f", "metadata": { "colab": { "base_uri": "https://localhost:8080/" }, "id": "37f99b61-55a6-4016-a697-bf065a083c7f", "outputId": "791c495f-3ccd-4b6a-af64-0f3ba732663f" }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "freesurfer_example.ipynb qsmxt_example.ipynb\n", "mp2rage.nii\t\t sct_toolbox_example.ipynb\n", "nipype_module_example.ipynb\n" ] } ], "source": [ "!ls " ] }, { "cell_type": "markdown", "id": "5acb2cc6-19a0-4e45-b878-608559f6e1a3", "metadata": {}, "source": [ "# Run" ] }, { "cell_type": "code", "execution_count": null, "id": "86339f98-42a7-428c-960e-b08b96ba5dde", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "fs-check-version --s subjectname --o /tmp/tmp.T7LgKS\n", "Thu Jun 29 02:40:59 UTC 2023\n", "\n", "setenv SUBJECTS_DIR /home/jovyan/example-notebooks/structural_imaging/freesurfer_output\n", "cd /home/jovyan/example-notebooks/structural_imaging\n", "/opt/freesurfer-7.3.2/bin/fs-check-version --s subjectname --o /tmp/tmp.T7LgKS\n", "-rwxrwxr-x. 1 nobody nobody 18565 Aug 4 2022 /opt/freesurfer-7.3.2/bin/fs-check-version\n", "\n", "freesurfer-linux-centos8_x86_64-7.3.2-20220804-6354275\n", "$Id$\n", "Linux jupyter-stebo85 5.4.17-2136.309.5.el7uek.x86_64 #2 SMP Mon Jul 18 02:08:52 PDT 2022 x86_64 x86_64 x86_64 GNU/Linux\n", "pid 1399\n", "Current FS Version freesurfer-linux-centos8_x86_64-7.3.2-20220804-6354275\n", "Subject does not have a bstampfile, copying /opt/freesurfer-7.3.2/build-stamp.txt\n", "Subject FS Version: freesurfer-linux-centos8_x86_64-7.3.2-20220804-6354275\n", "No constraints on version because REQ=UnSet and FsVerFile=NotThere\n", "#@#% fs-check-version match = 1\n", "fs-check-version Done\n", "INFO: SUBJECTS_DIR is /home/jovyan/example-notebooks/structural_imaging/freesurfer_output\n", "Actual FREESURFER_HOME /usr/local/freesurfer/7.3.2-1\n", "Linux jupyter-stebo85 5.4.17-2136.309.5.el7uek.x86_64 #2 SMP Mon Jul 18 02:08:52 PDT 2022 x86_64 x86_64 x86_64 GNU/Linux\n", "/home/jovyan/example-notebooks/structural_imaging/freesurfer_output/subjectname\n", "\n", " mri_convert /home/jovyan/example-notebooks/structural_imaging/mp2rage.nii /home/jovyan/example-notebooks/structural_imaging/freesurfer_output/subjectname/mri/orig/001.mgz \n", "\n", "mri_convert /home/jovyan/example-notebooks/structural_imaging/mp2rage.nii /home/jovyan/example-notebooks/structural_imaging/freesurfer_output/subjectname/mri/orig/001.mgz \n", "reading from /home/jovyan/example-notebooks/structural_imaging/mp2rage.nii...\n", "TR=0.00, TE=0.00, TI=0.00, flip angle=0.00\n", "i_ras = (1, 0, 0)\n", "j_ras = (0, 1, 0)\n", "k_ras = (0, 0, 1)\n", "writing to /home/jovyan/example-notebooks/structural_imaging/freesurfer_output/subjectname/mri/orig/001.mgz...\n", "#--------------------------------------------\n", "#@# MotionCor Thu Jun 29 02:43:10 UTC 2023\n", "Found 1 runs\n", "/home/jovyan/example-notebooks/structural_imaging/freesurfer_output/subjectname/mri/orig/001.mgz\n", "Checking for (invalid) multi-frame inputs...\n", "Only one run found so motion\n", "correction will not be performed. I'll\n", "copy the run to rawavg and continue.\n", "\n", " cp /home/jovyan/example-notebooks/structural_imaging/freesurfer_output/subjectname/mri/orig/001.mgz /home/jovyan/example-notebooks/structural_imaging/freesurfer_output/subjectname/mri/rawavg.mgz \n", "\n", "\n", " mri_info /home/jovyan/example-notebooks/structural_imaging/freesurfer_output/subjectname/mri/rawavg.mgz \n", "\n", "rawavg.mgz ========================================\n", "Volume information for /home/jovyan/example-notebooks/structural_imaging/freesurfer_output/subjectname/mri/rawavg.mgz\n", " type: MGH\n", " dimensions: 640 x 750 x 800\n", " voxel sizes: 0.300000, 0.300000, 0.300000\n", " type: FLOAT (3)\n", " fov: 240.000\n", " dof: 1\n", " xstart: -96.0, xend: 96.0\n", " ystart: -112.5, yend: 112.5\n", " zstart: -120.0, zend: 120.0\n", " TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees\n", " nframes: 1\n", " PhEncDir: UNKNOWN\n", " FieldStrength: 0.000000\n", "ras xform present\n", " xform info: x_r = 1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.3750\n", " : x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = 0.3750\n", " : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 0.3750\n", "\n", "talairach xfm : \n", "Orientation : RAS\n", "Primary Slice Direction: axial\n", "\n", "voxel to ras transform:\n", " 0.3000 0.0000 0.0000 -95.6250\n", " 0.0000 0.3000 0.0000 -112.1250\n", " 0.0000 0.0000 0.3000 -119.6250\n", " 0.0000 0.0000 0.0000 1.0000\n", "\n", "voxel-to-ras determinant 0.027\n", "\n", "ras to voxel transform:\n", " 3.3333 0.0000 0.0000 318.7500\n", " 0.0000 3.3333 0.0000 373.7500\n", " 0.0000 0.0000 3.3333 398.7500\n", " 0.0000 0.0000 0.0000 1.0000\n", "/home/jovyan/example-notebooks/structural_imaging/freesurfer_output/subjectname\n", "\n", " mri_convert /home/jovyan/example-notebooks/structural_imaging/freesurfer_output/subjectname/mri/rawavg.mgz /home/jovyan/example-notebooks/structural_imaging/freesurfer_output/subjectname/mri/orig.mgz --conform \n", "\n", "mri_convert /home/jovyan/example-notebooks/structural_imaging/freesurfer_output/subjectname/mri/rawavg.mgz /home/jovyan/example-notebooks/structural_imaging/freesurfer_output/subjectname/mri/orig.mgz --conform \n", "reading from /home/jovyan/example-notebooks/structural_imaging/freesurfer_output/subjectname/mri/rawavg.mgz...\n", "TR=0.00, TE=0.00, TI=0.00, flip angle=0.00\n", "i_ras = (1, 0, 0)\n", "j_ras = (0, 1, 0)\n", "k_ras = (0, 0, 1)\n", "changing data type from float to uchar (noscale = 0)...\n", "MRIchangeType: Building histogram 0 255 1000, flo=0, fhi=0.999, dest_type=0\n", "Reslicing using trilinear interpolation \n", "writing to /home/jovyan/example-notebooks/structural_imaging/freesurfer_output/subjectname/mri/orig.mgz...\n", "\n", " mri_add_xform_to_header -c /home/jovyan/example-notebooks/structural_imaging/freesurfer_output/subjectname/mri/transforms/talairach.xfm /home/jovyan/example-notebooks/structural_imaging/freesurfer_output/subjectname/mri/orig.mgz /home/jovyan/example-notebooks/structural_imaging/freesurfer_output/subjectname/mri/orig.mgz \n", "\n", "INFO: extension is mgz\n", "\n", " mri_info /home/jovyan/example-notebooks/structural_imaging/freesurfer_output/subjectname/mri/orig.mgz \n", "\n", "orig.mgz ========================================\n", "Volume information for /home/jovyan/example-notebooks/structural_imaging/freesurfer_output/subjectname/mri/orig.mgz\n", " type: MGH\n", " dimensions: 256 x 256 x 256\n", " voxel sizes: 1.000000, 1.000000, 1.000000\n", " type: UCHAR (0)\n", " fov: 256.000\n", " dof: 1\n", " xstart: -128.0, xend: 128.0\n", " ystart: -128.0, yend: 128.0\n", " zstart: -128.0, zend: 128.0\n", " TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees\n", " nframes: 1\n", " PhEncDir: UNKNOWN\n", " FieldStrength: 0.000000\n", "ras xform present\n", " xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.3750\n", " : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.3750\n", " : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.3750\n", "\n", "talairach xfm : /home/jovyan/example-notebooks/structural_imaging/freesurfer_output/subjectname/mri/transforms/talairach.xfm\n", "Orientation : LIA\n", "Primary Slice Direction: coronal\n", "\n", "voxel to ras transform:\n", " -1.0000 0.0000 0.0000 128.3750\n", " 0.0000 0.0000 1.0000 -127.6250\n", " 0.0000 -1.0000 0.0000 128.3750\n", " 0.0000 0.0000 0.0000 1.0000\n", "\n", "voxel-to-ras determinant -1\n", "\n", "ras to voxel transform:\n", " -1.0000 -0.0000 -0.0000 128.3750\n", " -0.0000 -0.0000 -1.0000 128.3750\n", " -0.0000 1.0000 -0.0000 127.6250\n", " -0.0000 -0.0000 -0.0000 1.0000\n", "#--------------------------------------------\n", "#@# Talairach Thu Jun 29 02:47:13 UTC 2023\n", "/home/jovyan/example-notebooks/structural_imaging/freesurfer_output/subjectname/mri\n", "\n", " mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 \n", "\n", "/usr/bin/bc\n", "/home/jovyan/example-notebooks/structural_imaging/freesurfer_output/subjectname/mri\n", "/opt/freesurfer-7.3.2/bin/mri_nu_correct.mni\n", "--no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50\n", "nIters 1\n", "mri_nu_correct.mni 7.3.2\n", "Linux jupyter-stebo85 5.4.17-2136.309.5.el7uek.x86_64 #2 SMP Mon Jul 18 02:08:52 PDT 2022 x86_64 x86_64 x86_64 GNU/Linux\n", "Thu Jun 29 02:47:13 UTC 2023\n", "tmpdir is ./tmp.mri_nu_correct.mni.1723\n", "cd /home/jovyan/example-notebooks/structural_imaging/freesurfer_output/subjectname/mri\n", "AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.1723/nu0.mgz --dtype uchar\n", "AntsN4BiasFieldCorrectionFs done\n", "mri_convert ./tmp.mri_nu_correct.mni.1723/nu0.mgz orig_nu.mgz --like orig.mgz --conform\n", "mri_convert ./tmp.mri_nu_correct.mni.1723/nu0.mgz orig_nu.mgz --like orig.mgz --conform \n", "reading from ./tmp.mri_nu_correct.mni.1723/nu0.mgz...\n", "TR=0.00, TE=0.00, TI=0.00, flip angle=0.00\n", "i_ras = (-1, 0, 0)\n", "j_ras = (0, 0, -1)\n", "k_ras = (0, 1, 0)\n", "INFO: transform src into the like-volume: orig.mgz\n", "writing to orig_nu.mgz...\n", " \n", " \n", "Thu Jun 29 02:50:27 UTC 2023\n", "mri_nu_correct.mni done\n", "\n", " talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm \n", "\n", "talairach_avi log file is transforms/talairach_avi.log...\n", "mv -f /home/jovyan/example-notebooks/structural_imaging/freesurfer_output/subjectname/mri/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt /home/jovyan/example-notebooks/structural_imaging/freesurfer_output/subjectname/mri/transforms/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt\n", "Started at Thu Jun 29 02:50:27 UTC 2023\n", "Ended at Thu Jun 29 02:51:13 UTC 2023\n", "talairach_avi done\n", "\n", " cp transforms/talairach.auto.xfm transforms/talairach.xfm \n", "\n", "lta_convert --src orig.mgz --trg /opt/freesurfer-7.3.2/average/mni305.cor.mgz --inxfm transforms/talairach.xfm --outlta transforms/talairach.xfm.lta --subject fsaverage --ltavox2vox\n", "7.3.2\n", "\n", "--src: orig.mgz src image (geometry).\n", "--trg: /opt/freesurfer-7.3.2/average/mni305.cor.mgz trg image (geometry).\n", "--inmni: transforms/talairach.xfm input MNI/XFM transform.\n", "--outlta: transforms/talairach.xfm.lta output LTA.\n", "--s: fsaverage subject name\n", "--ltavox2vox: output LTA as VOX_TO_VOX transform.\n", " LTA read, type : 1\n", " 1.07958 0.00270 -0.01574 0.58327;\n", " 0.01399 0.99838 0.31440 -9.30106;\n", " 0.00758 -0.40444 1.15055 -29.25244;\n", " 0.00000 0.00000 0.00000 1.00000;\n", "setting subject to fsaverage\n", "Writing LTA to file transforms/talairach.xfm.lta...\n", "lta_convert successful.\n", "~/example-notebooks/structural_imaging/freesurfer_output/subjectname/mri/transforms ~/example-notebooks/structural_imaging/freesurfer_output/subjectname/mri \n", "~/example-notebooks/structural_imaging/freesurfer_output/subjectname/mri \n", "#--------------------------------------------\n", "#@# Talairach Failure Detection Thu Jun 29 02:51:15 UTC 2023\n", "/home/jovyan/example-notebooks/structural_imaging/freesurfer_output/subjectname/mri\n", "\n", " talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n", "\n", "talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7053, pval=0.4932 >= threshold=0.0050)\n", "\n", " awk -f /opt/freesurfer-7.3.2/bin/extract_talairach_avi_QA.awk /home/jovyan/example-notebooks/structural_imaging/freesurfer_output/subjectname/mri/transforms/talairach_avi.log \n", "\n", "\n", " tal_QC_AZS /home/jovyan/example-notebooks/structural_imaging/freesurfer_output/subjectname/mri/transforms/talairach_avi.log \n", "\n", "TalAviQA: 0.97201\n", "z-score: -1\n", "#--------------------------------------------\n", "#@# Nu Intensity Correction Thu Jun 29 02:51:15 UTC 2023\n", "\n", " mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 \n", "\n", "/usr/bin/bc\n", "/home/jovyan/example-notebooks/structural_imaging/freesurfer_output/subjectname/mri\n", "/opt/freesurfer-7.3.2/bin/mri_nu_correct.mni\n", "--i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4\n", "nIters 2\n", "mri_nu_correct.mni 7.3.2\n", "Linux jupyter-stebo85 5.4.17-2136.309.5.el7uek.x86_64 #2 SMP Mon Jul 18 02:08:52 PDT 2022 x86_64 x86_64 x86_64 GNU/Linux\n", "Thu Jun 29 02:51:15 UTC 2023\n", "tmpdir is ./tmp.mri_nu_correct.mni.1951\n", "cd /home/jovyan/example-notebooks/structural_imaging/freesurfer_output/subjectname/mri\n", "AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.1951/nu0.mgz --dtype uchar\n", "AntsN4BiasFieldCorrectionFs done\n", "mri_binarize --i ./tmp.mri_nu_correct.mni.1951/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.1951/ones.mgz\n", "\n", "7.3.2\n", "cwd /home/jovyan/example-notebooks/structural_imaging/freesurfer_output/subjectname/mri\n", "cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.1951/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.1951/ones.mgz \n", "sysname Linux\n", "hostname jupyter-stebo85\n", "machine x86_64\n", "user jovyan\n", "\n", "input ./tmp.mri_nu_correct.mni.1951/nu0.mgz\n", "frame 0\n", "nErode3d 0\n", "nErode2d 0\n", "output ./tmp.mri_nu_correct.mni.1951/ones.mgz\n", "Binarizing based on threshold\n", "min -1\n", "max +infinity\n", "binval 1\n", "binvalnot 0\n", "fstart = 0, fend = 0, nframes = 1\n", "Starting parallel 1\n", "Found 16777216 values in range\n", "Counting number of voxels in first frame\n", "Found 16777215 voxels in final mask\n", "Writing output to ./tmp.mri_nu_correct.mni.1951/ones.mgz\n", "Count: 16777215 16777215.000000 16777216 99.999994\n", "mri_binarize done\n", "mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.1951/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.1951/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1951/input.mean.dat\n", "\n", "7.3.2\n", "cwd \n", "cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.1951/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.1951/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1951/input.mean.dat \n", "sysname Linux\n", "hostname jupyter-stebo85\n", "machine x86_64\n", "user jovyan\n", "whitesurfname white\n", "UseRobust 0\n", "Loading ./tmp.mri_nu_correct.mni.1951/ones.mgz\n", "Loading orig.mgz\n", "Voxel Volume is 1 mm^3\n", "Generating list of segmentation ids\n", "Found 1 segmentations\n", "Computing statistics for each segmentation\n", "\n", "Reporting on 1 segmentations\n", "Using PrintSegStat\n", "Computing spatial average of each frame\n", "\n", "Writing to ./tmp.mri_nu_correct.mni.1951/input.mean.dat\n", "mri_segstats done\n", "mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.1951/ones.mgz --i ./tmp.mri_nu_correct.mni.1951/nu0.mgz --sum ./tmp.mri_nu_correct.mni.1951/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1951/output.mean.dat\n", "\n", "7.3.2\n", "cwd \n", "cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.1951/ones.mgz --i ./tmp.mri_nu_correct.mni.1951/nu0.mgz --sum ./tmp.mri_nu_correct.mni.1951/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1951/output.mean.dat \n", "sysname Linux\n", "hostname jupyter-stebo85\n", "machine x86_64\n", "user jovyan\n", "whitesurfname white\n", "UseRobust 0\n", "Loading ./tmp.mri_nu_correct.mni.1951/ones.mgz\n", "Loading ./tmp.mri_nu_correct.mni.1951/nu0.mgz\n", "Voxel Volume is 1 mm^3\n", "Generating list of segmentation ids\n", "Found 1 segmentations\n", "Computing statistics for each segmentation\n", "\n", "Reporting on 1 segmentations\n", "Using PrintSegStat\n", "Computing spatial average of each frame\n", "\n", "Writing to ./tmp.mri_nu_correct.mni.1951/output.mean.dat\n", "mri_segstats done\n", "mris_calc -o ./tmp.mri_nu_correct.mni.1951/nu0.mgz ./tmp.mri_nu_correct.mni.1951/nu0.mgz mul 1.16048835830789136545\n", "Saving result to './tmp.mri_nu_correct.mni.1951/nu0.mgz' (type = MGH ) [ ok ]\n", "mri_convert ./tmp.mri_nu_correct.mni.1951/nu0.mgz nu.mgz --like orig.mgz\n", "mri_convert ./tmp.mri_nu_correct.mni.1951/nu0.mgz nu.mgz --like orig.mgz \n", "reading from ./tmp.mri_nu_correct.mni.1951/nu0.mgz...\n", "TR=0.00, TE=0.00, TI=0.00, flip angle=0.00\n", "i_ras = (-1, 0, 0)\n", "j_ras = (0, 0, -1)\n", "k_ras = (0, 1, 0)\n", "INFO: transform src into the like-volume: orig.mgz\n", "writing to nu.mgz...\n", "mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz\n", "type change took 0 minutes and 7 seconds.\n", "FIRST_PERCENTILE 0.010000\n", "WM_PERCENTILE 0.900000\n", "MAX_R 50.000000\n", "i1 = 6, i2 = 82\n", "#mri_make_uchar# mapping 15 211 to 3 110 : b -5.93289 m 0.548893 : thresh 10.8088 maxsat 475.38 : nzero 12342897 nsat 0\n", " \n", " \n", "Thu Jun 29 02:55:31 UTC 2023\n", "mri_nu_correct.mni done\n", "\n", " mri_add_xform_to_header -c /home/jovyan/example-notebooks/structural_imaging/freesurfer_output/subjectname/mri/transforms/talairach.xfm nu.mgz nu.mgz \n", "\n", "INFO: extension is mgz\n", "#--------------------------------------------\n", "#@# Intensity Normalization Thu Jun 29 02:55:32 UTC 2023\n", "/home/jovyan/example-notebooks/structural_imaging/freesurfer_output/subjectname/mri\n", "\n", " mri_normalize -g 1 -seed 1234 -mprage nu.mgz T1.mgz \n", "\n", "using max gradient = 1.000\n", "setting seed for random number genererator to 1234\n", "assuming input volume is MGH (Van der Kouwe) MP-RAGE\n", "reading mri_src from nu.mgz...\n", "normalizing image...\n", "NOT doing gentle normalization with control points/label\n", "talairach transform\n", " 1.07958 0.00270 -0.01574 0.58327;\n", " 0.01399 0.99838 0.31440 -9.30106;\n", " 0.00758 -0.40444 1.15055 -29.25244;\n", " 0.00000 0.00000 0.00000 1.00000;\n", "processing without aseg, no1d=0\n", "MRInormInit(): \n", "INFO: Modifying talairach volume c_(r,a,s) based on average_305\n", "MRInormalize(): \n", "MRIsplineNormalize(): npeaks = 19\n", "Starting OpenSpline(): npoints = 19\n", "building Voronoi diagram...\n", "performing soap bubble smoothing, sigma = 8...\n", "\n", "Iterating 2 times\n", "---------------------------------\n", "3d normalization pass 1 of 2\n", "white matter peak found at 110\n", "white matter peak found at 110\n", "gm peak at 62 (62), valley at 51 (51)\n", "csf peak at 32, setting threshold to 52\n", "building Voronoi diagram...\n", "performing soap bubble smoothing, sigma = 8...\n", "---------------------------------\n", "3d normalization pass 2 of 2\n", "white matter peak found at 110\n", "white matter peak found at 110\n", "gm peak at 65 (65), valley at 53 (53)\n", "csf peak at 33, setting threshold to 54\n", "building Voronoi diagram...\n", "performing soap bubble smoothing, sigma = 8...\n", "Done iterating ---------------------------------\n", "writing output to T1.mgz\n", "3D bias adjustment took 2 minutes and 10 seconds.\n", "#--------------------------------------------\n", "#@# Skull Stripping Thu Jun 29 02:57:44 UTC 2023\n", "/home/jovyan/example-notebooks/structural_imaging/freesurfer_output/subjectname/mri\n", "\n", " mri_em_register -skull nu.mgz /opt/freesurfer-7.3.2/average/RB_all_withskull_2020_01_02.gca transforms/talairach_with_skull.lta \n", "\n", "aligning to atlas containing skull, setting unknown_nbr_spacing = 5\n", "\n", "== Number of threads available to mri_em_register for OpenMP = 1 == \n", "reading 1 input volumes...\n", "logging results to talairach_with_skull.log\n", "reading '/opt/freesurfer-7.3.2/average/RB_all_withskull_2020_01_02.gca'...\n", "GCAread took 0 minutes and 1 seconds.\n", "average std = 23.0 using min determinant for regularization = 52.8\n", "0 singular and 9205 ill-conditioned covariance matrices regularized\n", "reading 'nu.mgz'...\n", "freeing gibbs priors...done.\n", "accounting for voxel sizes in initial transform\n", "bounding unknown intensity as < 8.9 or > 556.0 \n", "total sample mean = 77.3 (1403 zeros)\n", "************************************************\n", "spacing=8, using 3292 sample points, tol=1.00e-05...\n", "************************************************\n", "register_mri: find_optimal_transform\n", "find_optimal_transform: nsamples 3292, passno 0, spacing 8\n", "resetting wm mean[0]: 100 --> 108\n", "resetting gm mean[0]: 61 --> 61\n", "input volume #1 is the most T1-like\n", "using real data threshold=25.0\n", "skull bounding box = (51, 29, 17) --> (205, 241, 220)\n", "finding center of left hemi white matter\n", "using (102, 100, 119) as brain centroid of Right_Cerebral_White_Matter...\n", "MRImask(): AllowDiffGeom = 1\n", "mean wm in atlas = 108, using box (83,74,94) --> (120, 126,144) to find MRI wm\n", "before smoothing, mri peak at 107\n", "robust fit to distribution - 107 +- 3.7\n", "after smoothing, mri peak at 107, scaling input intensities by 1.009\n", "scaling channel 0 by 1.00935\n", "initial log_p = -4.355\n", "************************************************\n", "First Search limited to translation only.\n", "************************************************\n", "max log p = -4.327209 @ (-10.526, 10.526, -10.526)\n", "max log p = -4.238077 @ (5.263, 5.263, 5.263)\n", "max log p = -4.103386 @ (2.632, -2.632, -2.632)\n", "max log p = -4.103386 @ (0.000, 0.000, 0.000)\n", "max log p = -4.087552 @ (-0.658, -0.658, -1.974)\n", "max log p = -4.087552 @ (0.000, 0.000, 0.000)\n", "max log p = -4.087552 @ (0.000, 0.000, 0.000)\n", "max log p = -4.087552 @ (0.000, 0.000, 0.000)\n", "Found translation: (-3.3, 12.5, -9.9): log p = -4.088\n", "****************************************\n", "Nine parameter search. iteration 0 nscales = 0 ...\n", "****************************************\n", "Result so far: scale 1.000: max_log_p=-3.772, old_max_log_p =-4.088 (thresh=-4.1)\n", " 1.06375 0.00000 0.00000 -11.47446;\n", " 0.00000 1.11081 0.29764 -30.89916;\n", " 0.00000 -0.27532 1.02750 26.07788;\n", " 0.00000 0.00000 0.00000 1.00000;\n", "iteration took 1 minutes and 35 seconds.\n", "****************************************\n", "Nine parameter search. iteration 1 nscales = 0 ...\n", "****************************************\n", "Result so far: scale 1.000: max_log_p=-3.772, old_max_log_p =-3.772 (thresh=-3.8)\n", " 1.06375 0.00000 0.00000 -11.47446;\n", " 0.00000 1.11081 0.29764 -30.89916;\n", " 0.00000 -0.27532 1.02750 26.07788;\n", " 0.00000 0.00000 0.00000 1.00000;\n", "reducing scale to 0.2500\n", "iteration took 1 minutes and 28 seconds.\n", "****************************************\n", "Nine parameter search. iteration 2 nscales = 1 ...\n", "****************************************\n", "Result so far: scale 0.250: max_log_p=-3.654, old_max_log_p =-3.772 (thresh=-3.8)\n", " 1.04325 -0.00851 0.03175 -11.59169;\n", " 0.00000 1.08921 0.29185 -25.65857;\n", "-0.03480 -0.26485 0.98844 30.03328;\n", " 0.00000 0.00000 0.00000 1.00000;\n", "iteration took 1 minutes and 22 seconds.\n", "****************************************\n", "Nine parameter search. iteration 3 nscales = 1 ...\n", "****************************************\n", "Result so far: scale 0.250: max_log_p=-3.648, old_max_log_p =-3.654 (thresh=-3.7)\n", " 1.04325 -0.00851 0.03175 -11.59169;\n", "-0.00116 1.10021 0.33011 -31.41711;\n", "-0.03479 -0.30035 0.97836 35.56596;\n", " 0.00000 0.00000 0.00000 1.00000;\n", "iteration took 1 minutes and 22 seconds.\n", "****************************************\n", "Nine parameter search. iteration 4 nscales = 1 ...\n", "****************************************\n", "Result so far: scale 0.250: max_log_p=-3.647, old_max_log_p =-3.648 (thresh=-3.6)\n", " 1.04383 0.00132 -0.00028 -9.04488;\n", "-0.00118 1.12083 0.33630 -32.79573;\n", "-0.00063 -0.30047 0.97888 31.13393;\n", " 0.00000 0.00000 0.00000 1.00000;\n", "reducing scale to 0.0625\n", "iteration took 1 minutes and 22 seconds.\n", "****************************************\n", "Nine parameter search. iteration 5 nscales = 2 ...\n", "****************************************\n", "Result so far: scale 0.062: max_log_p=-3.626, old_max_log_p =-3.647 (thresh=-3.6)\n", " 1.04240 0.01742 0.01298 -11.43840;\n", "-0.01818 1.12155 0.31881 -29.55735;\n", "-0.00921 -0.28194 0.98426 28.90162;\n", " 0.00000 0.00000 0.00000 1.00000;\n", "iteration took 1 minutes and 18 seconds.\n", "****************************************\n", "Nine parameter search. iteration 6 nscales = 2 ...\n", "****************************************\n", "Result so far: scale 0.062: max_log_p=-3.625, old_max_log_p =-3.626 (thresh=-3.6)\n", " 1.04107 0.01509 0.02101 -12.41482;\n", "-0.01816 1.12024 0.31844 -29.82493;\n", "-0.01776 -0.28240 0.98528 29.92633;\n", " 0.00000 0.00000 0.00000 1.00000;\n", "min search scale 0.025000 reached\n", "***********************************************\n", "Computing MAP estimate using 3292 samples...\n", "***********************************************\n", "dt = 5.00e-06, momentum=0.80, tol=1.00e-05\n", "l_intensity = 1.0000\n", "Aligning input volume to GCA...\n", "Transform matrix\n", " 1.04107 0.01509 0.02101 -12.41482;\n", "-0.01816 1.12024 0.31844 -29.82493;\n", "-0.01776 -0.28240 0.98528 29.92633;\n", " 0.00000 0.00000 0.00000 1.00000;\n", "nsamples 3292\n", "Quasinewton: input matrix\n", " 1.04107 0.01509 0.02101 -12.41482;\n", "-0.01816 1.12024 0.31844 -29.82493;\n", "-0.01776 -0.28240 0.98528 29.92633;\n", " 0.00000 0.00000 0.00000 1.00000;\n", " IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010\n", "Resulting transform:\n", " 1.04107 0.01509 0.02101 -12.41482;\n", "-0.01816 1.12024 0.31844 -29.82493;\n", "-0.01776 -0.28240 0.98528 29.92633;\n", " 0.00000 0.00000 0.00000 1.00000;\n", "\n", "pass 1, spacing 8: log(p) = -3.625 (old=-4.355)\n", "transform before final EM align:\n", " 1.04107 0.01509 0.02101 -12.41482;\n", "-0.01816 1.12024 0.31844 -29.82493;\n", "-0.01776 -0.28240 0.98528 29.92633;\n", " 0.00000 0.00000 0.00000 1.00000;\n", "\n", "**************************************************\n", " EM alignment process ...\n", " Computing final MAP estimate using 364986 samples. \n", "**************************************************\n", "dt = 5.00e-06, momentum=0.80, tol=1.00e-07\n", "l_intensity = 1.0000\n", "Aligning input volume to GCA...\n", "Transform matrix\n", " 1.04107 0.01509 0.02101 -12.41482;\n", "-0.01816 1.12024 0.31844 -29.82493;\n", "-0.01776 -0.28240 0.98528 29.92633;\n", " 0.00000 0.00000 0.00000 1.00000;\n", "nsamples 364986\n", "Quasinewton: input matrix\n", " 1.04107 0.01509 0.02101 -12.41482;\n", "-0.01816 1.12024 0.31844 -29.82493;\n", "-0.01776 -0.28240 0.98528 29.92633;\n", " 0.00000 0.00000 0.00000 1.00000;\n", " IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = 4.1 tol 0.000000\n", "final transform:\n", " 1.04107 0.01509 0.02101 -12.41482;\n", "-0.01816 1.12024 0.31844 -29.82493;\n", "-0.01776 -0.28240 0.98528 29.92633;\n", " 0.00000 0.00000 0.00000 1.00000;\n", "\n", "writing output transformation to transforms/talairach_with_skull.lta...\n", "#VMPC# mri_em_register VmPeak 800756\n", "FSRUNTIME@ mri_em_register 0.1833 hours 1 threads\n", "registration took 11 minutes and 0 seconds.\n", "\n", " mri_watershed -T1 -brain_atlas /opt/freesurfer-7.3.2/average/RB_all_withskull_2020_01_02.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz \n", "\n", "\n", "Mode: T1 normalized volume\n", "Mode: Use the information of atlas (default parms, --help for details)\n", "\n", "*********************************************************\n", "The input file is T1.mgz\n", "The output file is brainmask.auto.mgz\n", "Weighting the input with atlas information before watershed\n", "\n", "*************************WATERSHED**************************\n", "Sorting...\n", " first estimation of the COG coord: x=129 y=99 z=114 r=79\n", " first estimation of the main basin volume: 2144899 voxels\n", " Looking for seedpoints \n", " 2 found in the cerebellum \n", " 16 found in the rest of the brain \n", " global maximum in x=106, y=92, z=76, Imax=255\n", " CSF=12, WM_intensity=110, WM_VARIANCE=5\n", " WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 \n", " preflooding height equal to 10 percent\n", "done.\n", "Analyze...\n", "\n", " main basin size=2229910857 voxels, voxel volume =1.000 \n", " = 2229910857 mmm3 = 2229910.784 cm3\n", "done.\n", "PostAnalyze...Basin Prior\n", " 8 basins merged thanks to atlas \n", " ***** 0 basin(s) merged in 1 iteration(s)\n", " ***** 0 voxel(s) added to the main basin\n", "done.\n", "Weighting the input with prior template \n", "\n", "****************TEMPLATE DEFORMATION****************\n", "\n", " second estimation of the COG coord: x=128,y=106, z=109, r=9955 iterations\n", "^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^\n", "\n", " GLOBAL CSF_MIN=0, CSF_intensity=7, CSF_MAX=21 , nb = 44406\n", " RIGHT_CER CSF_MIN=0, CSF_intensity=4, CSF_MAX=11 , nb = 3024\n", " LEFT_CER CSF_MIN=0, CSF_intensity=4, CSF_MAX=11 , nb = 3060\n", " RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=20 , nb = 18684\n", " LEFT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=21 , nb = 18684\n", " OTHER CSF_MIN=0, CSF_intensity=4, CSF_MAX=14 , nb = 954\n", " Problem with the least square interpolation in GM_MIN calculation.\n", " \n", " CSF_MAX TRANSITION GM_MIN GM\n", " GLOBAL \n", " before analyzing : 21, 23, 31, 64\n", " after analyzing : 21, 28, 31, 37\n", " RIGHT_CER \n", " before analyzing : 11, 16, 36, 64\n", " after analyzing : 11, 29, 36, 37\n", " LEFT_CER \n", " before analyzing : 11, 16, 37, 61\n", " after analyzing : 11, 30, 37, 37\n", " RIGHT_BRAIN \n", " before analyzing : 20, 22, 29, 64\n", " after analyzing : 20, 26, 29, 35\n", " LEFT_BRAIN \n", " before analyzing : 21, 24, 32, 64\n", " after analyzing : 21, 29, 32, 37\n", " OTHER \n", " before analyzing : 14, 15, 27, 94\n", " after analyzing : 14, 23, 27, 40\n", " mri_strip_skull: done peeling brain\n", " highly tesselated surface with 10242 vertices\n", " matching...65 iterations\n", "\n", "*********************VALIDATION*********************\n", "curvature mean = -0.013, std = 0.011\n", "curvature mean = 69.801, std = 8.241\n", "\n", "No Rigid alignment: -atlas Mode Off (basic atlas / no registration)\n", " before rotation: sse = 2.23, sigma = 3.29\n", " after rotation: sse = 2.23, sigma = 3.29\n", "Localization of inacurate regions: Erosion-Dilation steps\n", " the sse mean is 2.27, its var is 2.73 \n", " before Erosion-Dilatation 0.09% of inacurate vertices\n", " after Erosion-Dilatation 0.00% of inacurate vertices\n", " Validation of the shape of the surface done.\n", "Scaling of atlas fields onto current surface fields\n", "\n", "********FINAL ITERATIVE TEMPLATE DEFORMATION********\n", "Compute Local values csf/gray\n", "Fine Segmentation...34 iterations\n", "\n", " mri_strip_skull: done peeling brain\n", "\n", "Brain Size = 1611792 voxels, voxel volume = 1.000 mm3\n", " = 1611792 mmm3 = 1611.792 cm3\n", "\n", "\n", "******************************\n", "Saving brainmask.auto.mgz\n", "done\n", "mri_watershed done\n", "\n", " cp brainmask.auto.mgz brainmask.mgz \n", "\n", "#-------------------------------------\n", "#@# EM Registration Thu Jun 29 03:09:01 UTC 2023\n", "/home/jovyan/example-notebooks/structural_imaging/freesurfer_output/subjectname/mri\n", "\n", " mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /opt/freesurfer-7.3.2/average/RB_all_2020-01-02.gca transforms/talairach.lta \n", "\n", "setting unknown_nbr_spacing = 3\n", "using MR volume brainmask.mgz to mask input volume...\n", "\n", "== Number of threads available to mri_em_register for OpenMP = 1 == \n", "reading 1 input volumes...\n", "logging results to talairach.log\n", "reading '/opt/freesurfer-7.3.2/average/RB_all_2020-01-02.gca'...\n", "GCAread took 0 minutes and 1 seconds.\n", "average std = 7.2 using min determinant for regularization = 5.2\n", "0 singular and 884 ill-conditioned covariance matrices regularized\n", "reading 'nu.mgz'...\n", "MRImask(): AllowDiffGeom = 1\n", "MRImask(): AllowDiffGeom = 1\n", "MRImask(): AllowDiffGeom = 1\n", "MRImask(): AllowDiffGeom = 1\n", "MRImask(): AllowDiffGeom = 1\n", "freeing gibbs priors...done.\n", "accounting for voxel sizes in initial transform\n", "bounding unknown intensity as < 5.9 or > 519.0 \n", "total sample mean = 79.1 (1017 zeros)\n", "************************************************\n", "spacing=8, using 2841 sample points, tol=1.00e-05...\n", "************************************************\n", "register_mri: find_optimal_transform\n", "find_optimal_transform: nsamples 2841, passno 0, spacing 8\n", "resetting wm mean[0]: 98 --> 107\n", "resetting gm mean[0]: 61 --> 61\n", "input volume #1 is the most T1-like\n", "using real data threshold=20.9\n", "skull bounding box = (62, 44, 31) --> (194, 181, 196)\n", "finding center of left hemi white matter\n", "using (106, 90, 114) as brain centroid of Right_Cerebral_White_Matter...\n", "MRImask(): AllowDiffGeom = 1\n", "mean wm in atlas = 107, using box (90,73,94) --> (122, 106,134) to find MRI wm\n", "before smoothing, mri peak at 107\n", "robust fit to distribution - 107 +- 3.2\n", "after smoothing, mri peak at 107, scaling input intensities by 1.000\n", "scaling channel 0 by 1\n", "initial log_p = -4.170\n", "************************************************\n", "First Search limited to translation only.\n", "************************************************\n", "max log p = -4.041770 @ (-10.526, 10.526, -10.526)\n", "max log p = -3.763349 @ (5.263, 5.263, 5.263)\n", "max log p = -3.695452 @ (2.632, -2.632, -2.632)\n", "max log p = -3.663278 @ (1.316, 3.947, 1.316)\n", "max log p = -3.653469 @ (-0.658, -0.658, -0.658)\n", "max log p = -3.653469 @ (0.000, 0.000, 0.000)\n", "max log p = -3.653469 @ (0.000, 0.000, 0.000)\n", "max log p = -3.653469 @ (0.000, 0.000, 0.000)\n", "Found translation: (-2.0, 16.4, -7.2): log p = -3.653\n", "****************************************\n", "Nine parameter search. iteration 0 nscales = 0 ...\n", "****************************************\n", "Result so far: scale 1.000: max_log_p=-3.190, old_max_log_p =-3.653 (thresh=-3.6)\n", " 1.07500 0.00000 0.00000 -11.63188;\n", " 0.00000 1.11081 0.29764 -28.48080;\n", " 0.00000 -0.25882 0.96593 30.71957;\n", " 0.00000 0.00000 0.00000 1.00000;\n", "iteration took 1 minutes and 20 seconds.\n", "****************************************\n", "Nine parameter search. iteration 1 nscales = 0 ...\n", "****************************************\n", "Result so far: scale 1.000: max_log_p=-3.190, old_max_log_p =-3.190 (thresh=-3.2)\n", " 1.07500 0.00000 0.00000 -11.63188;\n", " 0.00000 1.11081 0.29764 -28.48080;\n", " 0.00000 -0.25882 0.96593 30.71957;\n", " 0.00000 0.00000 0.00000 1.00000;\n", "reducing scale to 0.2500\n", "iteration took 1 minutes and 19 seconds.\n", "****************************************\n", "Nine parameter search. iteration 2 nscales = 1 ...\n", "****************************************\n", "Result so far: scale 0.250: max_log_p=-3.104, old_max_log_p =-3.190 (thresh=-3.2)\n", " 1.05409 0.00000 0.00000 -8.93891;\n", " 0.00000 1.15247 0.30880 -34.02222;\n", " 0.00000 -0.26367 0.98404 27.44393;\n", " 0.00000 0.00000 0.00000 1.00000;\n", "iteration took 1 minutes and 19 seconds.\n", "****************************************\n", "Nine parameter search. iteration 3 nscales = 1 ...\n", "****************************************\n", "Result so far: scale 0.250: max_log_p=-3.104, old_max_log_p =-3.104 (thresh=-3.1)\n", " 1.05409 0.00000 0.00000 -8.93891;\n", " 0.00000 1.15247 0.30880 -34.02222;\n", " 0.00000 -0.26367 0.98404 27.44393;\n", " 0.00000 0.00000 0.00000 1.00000;\n", "reducing scale to 0.0625\n", "iteration took 1 minutes and 16 seconds.\n", "****************************************\n", "Nine parameter search. iteration 4 nscales = 2 ...\n", "****************************************\n", "Result so far: scale 0.062: max_log_p=-3.052, old_max_log_p =-3.104 (thresh=-3.1)\n", " 1.05652 -0.00215 0.00803 -9.89662;\n", " 0.00000 1.14977 0.30808 -33.66290;\n", "-0.00863 -0.26274 0.98055 28.36465;\n", " 0.00000 0.00000 0.00000 1.00000;\n", "iteration took 1 minutes and 21 seconds.\n", "****************************************\n", "Nine parameter search. iteration 5 nscales = 2 ...\n", "****************************************\n", "Result so far: scale 0.062: max_log_p=-3.052, old_max_log_p =-3.052 (thresh=-3.0)\n", " 1.05652 -0.00215 0.00803 -9.89662;\n", " 0.00000 1.14977 0.30808 -33.66290;\n", "-0.00863 -0.26274 0.98055 28.36465;\n", " 0.00000 0.00000 0.00000 1.00000;\n", "min search scale 0.025000 reached\n", "***********************************************\n", "Computing MAP estimate using 2841 samples...\n", "***********************************************\n", "dt = 5.00e-06, momentum=0.80, tol=1.00e-05\n", "l_intensity = 1.0000\n", "Aligning input volume to GCA...\n", "Transform matrix\n", " 1.05652 -0.00215 0.00803 -9.89662;\n", " 0.00000 1.14977 0.30808 -33.66290;\n", "-0.00863 -0.26274 0.98055 28.36465;\n", " 0.00000 0.00000 0.00000 1.00000;\n", "nsamples 2841\n", "Quasinewton: input matrix\n", " 1.05652 -0.00215 0.00803 -9.89662;\n", " 0.00000 1.14977 0.30808 -33.66290;\n", "-0.00863 -0.26274 0.98055 28.36465;\n", " 0.00000 0.00000 0.00000 1.00000;\n", " IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010\n", "Resulting transform:\n", " 1.05652 -0.00215 0.00803 -9.89662;\n", " 0.00000 1.14977 0.30808 -33.66290;\n", "-0.00863 -0.26274 0.98055 28.36465;\n", " 0.00000 0.00000 0.00000 1.00000;\n", "\n", "pass 1, spacing 8: log(p) = -3.052 (old=-4.170)\n", "transform before final EM align:\n", " 1.05652 -0.00215 0.00803 -9.89662;\n", " 0.00000 1.14977 0.30808 -33.66290;\n", "-0.00863 -0.26274 0.98055 28.36465;\n", " 0.00000 0.00000 0.00000 1.00000;\n", "\n", "**************************************************\n", " EM alignment process ...\n", " Computing final MAP estimate using 315638 samples. \n", "**************************************************\n", "dt = 5.00e-06, momentum=0.80, tol=1.00e-07\n", "l_intensity = 1.0000\n", "Aligning input volume to GCA...\n", "Transform matrix\n", " 1.05652 -0.00215 0.00803 -9.89662;\n", " 0.00000 1.14977 0.30808 -33.66290;\n", "-0.00863 -0.26274 0.98055 28.36465;\n", " 0.00000 0.00000 0.00000 1.00000;\n", "nsamples 315638\n", "Quasinewton: input matrix\n", " 1.05652 -0.00215 0.00803 -9.89662;\n", " 0.00000 1.14977 0.30808 -33.66290;\n", "-0.00863 -0.26274 0.98055 28.36465;\n", " 0.00000 0.00000 0.00000 1.00000;\n", " IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = 3.7 tol 0.000000\n", "final transform:\n", " 1.05652 -0.00215 0.00803 -9.89662;\n", " 0.00000 1.14977 0.30808 -33.66290;\n", "-0.00863 -0.26274 0.98055 28.36465;\n", " 0.00000 0.00000 0.00000 1.00000;\n", "\n", "writing output transformation to transforms/talairach.lta...\n", "#VMPC# mri_em_register VmPeak 788204\n", "FSRUNTIME@ mri_em_register 0.1472 hours 1 threads\n", "registration took 8 minutes and 50 seconds.\n", "#--------------------------------------\n", "#@# CA Normalize Thu Jun 29 03:17:51 UTC 2023\n", "/home/jovyan/example-notebooks/structural_imaging/freesurfer_output/subjectname/mri\n", "\n", " mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /opt/freesurfer-7.3.2/average/RB_all_2020-01-02.gca transforms/talairach.lta norm.mgz \n", "\n", "writing control point volume to ctrl_pts.mgz\n", "using MR volume brainmask.mgz to mask input volume...\n", "reading 1 input volume\n", "reading atlas from '/opt/freesurfer-7.3.2/average/RB_all_2020-01-02.gca'...\n", "reading transform from 'transforms/talairach.lta'...\n", "reading input volume from nu.mgz...\n", "resetting wm mean[0]: 98 --> 107\n", "resetting gm mean[0]: 61 --> 61\n", "input volume #1 is the most T1-like\n", "using real data threshold=20.9\n", "skull bounding box = (62, 44, 31) --> (194, 181, 196)\n", "finding center of left hemi white matter\n", "using (106, 90, 114) as brain centroid of Right_Cerebral_White_Matter...\n", "mean wm in atlas = 107, using box (90,73,94) --> (122, 106,134) to find MRI wm\n", "before smoothing, mri peak at 107\n", "robust fit to distribution - 107 +- 3.2\n", "after smoothing, mri peak at 107, scaling input intensities by 1.000\n", "scaling channel 0 by 1\n", "using 246437 sample points...\n", "INFO: compute sample coordinates transform\n", " 1.05652 -0.00215 0.00803 -9.89662;\n", " 0.00000 1.14977 0.30808 -33.66290;\n", "-0.00863 -0.26274 0.98055 28.36465;\n", " 0.00000 0.00000 0.00000 1.00000;\n", "INFO: transform used\n", "finding control points in Left_Cerebral_White_Matter....\n", "found 40230 control points for structure...\n", "bounding box (129, 48, 34) --> (191, 150, 194)\n", "Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0\n", "20 of 9292 (0.2%) samples deleted\n", "finding control points in Right_Cerebral_White_Matter....\n", "found 39478 control points for structure...\n", "bounding box (67, 47, 32) --> (130, 143, 195)\n", "Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 132.0\n", "17 of 9476 (0.2%) samples deleted\n", "finding control points in Left_Cerebellum_White_Matter....\n", "found 3105 control points for structure...\n", "bounding box (130, 124, 62) --> (176, 163, 115)\n", "Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0\n", "0 of 352 (0.0%) samples deleted\n", "finding control points in Right_Cerebellum_White_Matter....\n", "found 2710 control points for structure...\n", "bounding box (87, 124, 59) --> (128, 162, 115)\n", "Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0\n", "2 of 393 (0.5%) samples deleted\n", "finding control points in Brain_Stem....\n", "found 3475 control points for structure...\n", "bounding box (113, 114, 97) --> (145, 173, 125)\n", "Brain_Stem: limiting intensities to 88.0 --> 132.0\n", "0 of 523 (0.0%) samples deleted\n", "using 20036 total control points for intensity normalization...\n", "bias field = 0.973 +- 0.051\n", "189 of 19997 control points discarded\n", "finding control points in Left_Cerebral_White_Matter....\n", "found 40230 control points for structure...\n", "bounding box (129, 48, 34) --> (191, 150, 194)\n", "Left_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0\n", "30 of 9460 (0.3%) samples deleted\n", "finding control points in Right_Cerebral_White_Matter....\n", "found 39478 control points for structure...\n", "bounding box (67, 47, 32) --> (130, 143, 195)\n", "Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0\n", "20 of 9622 (0.2%) samples deleted\n", "finding control points in Left_Cerebellum_White_Matter....\n", "found 3105 control points for structure...\n", "bounding box (130, 124, 62) --> (176, 163, 115)\n", "Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0\n", "158 of 479 (33.0%) samples deleted\n", "finding control points in Right_Cerebellum_White_Matter....\n", "found 2710 control points for structure...\n", "bounding box (87, 124, 59) --> (128, 162, 115)\n", "Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0\n", "157 of 462 (34.0%) samples deleted\n", "finding control points in Brain_Stem....\n", "found 3475 control points for structure...\n", "bounding box (113, 114, 97) --> (145, 173, 125)\n", "Brain_Stem: limiting intensities to 88.0 --> 132.0\n", "40 of 600 (6.7%) samples deleted\n", "using 20623 total control points for intensity normalization...\n", "bias field = 1.029 +- 0.049\n", "175 of 20122 control points discarded\n", "finding control points in Left_Cerebral_White_Matter....\n", "found 40230 control points for structure...\n", "bounding box (129, 48, 34) --> (191, 150, 194)\n", "Left_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0\n", "21 of 9495 (0.2%) samples deleted\n", "finding control points in Right_Cerebral_White_Matter....\n", "found 39478 control points for structure...\n", "bounding box (67, 47, 32) --> (130, 143, 195)\n", "Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0\n", "29 of 9631 (0.3%) samples deleted\n", "finding control points in Left_Cerebellum_White_Matter....\n", "found 3105 control points for structure...\n", "bounding box (130, 124, 62) --> (176, 163, 115)\n", "Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0\n", "245 of 503 (48.7%) samples deleted\n", "finding control points in Right_Cerebellum_White_Matter....\n", "found 2710 control points for structure...\n", "bounding box (87, 124, 59) --> (128, 162, 115)\n", "Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0\n", "274 of 465 (58.9%) samples deleted\n", "finding control points in Brain_Stem....\n", "found 3475 control points for structure...\n", "bounding box (113, 114, 97) --> (145, 173, 125)\n", "Brain_Stem: limiting intensities to 88.0 --> 132.0\n", "88 of 638 (13.8%) samples deleted\n", "using 20732 total control points for intensity normalization...\n", "bias field = 1.028 +- 0.043\n", "159 of 19866 control points discarded\n", "writing normalized volume to norm.mgz...\n", "writing control points to ctrl_pts.mgz\n", "freeing GCA...done.\n", "normalization took 1 minutes and 30 seconds.\n", "#--------------------------------------\n", "#@# CA Reg Thu Jun 29 03:19:21 UTC 2023\n", "/home/jovyan/example-notebooks/structural_imaging/freesurfer_output/subjectname/mri\n", "\n", " mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /opt/freesurfer-7.3.2/average/RB_all_2020-01-02.gca transforms/talairach.m3z \n", "\n", "not handling expanded ventricles...\n", "using previously computed transform transforms/talairach.lta\n", "renormalizing sequences with structure alignment, equivalent to:\n", "\t-renormalize\n", "\t-regularize_mean 0.500\n", "\t-regularize 0.500\n", "using MR volume brainmask.mgz to mask input volume...\n", "\n", "== Number of threads available to mri_ca_register for OpenMP = 1 == \n", "reading 1 input volumes...\n", "logging results to talairach.log\n", "reading input volume 'norm.mgz'...\n", "reading GCA '/opt/freesurfer-7.3.2/average/RB_all_2020-01-02.gca'...\n", "label assignment complete, 0 changed (0.00%)\n", "freeing gibbs priors...done.\n", "average std[0] = 5.0\n", "Starting GCAMregister()\n", "label assignment complete, 0 changed (0.00%)\n", "npasses = 1, nlevels = 6\n", "#pass# 1 of 1 ************************\n", "enabling zero nodes\n", "setting smoothness cost coefficient to 0.156\n", "\n", "#GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2\n", "l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.16 \n", "tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=no\n", "\n", "blurring input image with Gaussian with sigma=2.000...\n", "GCAMRegisterLevel(): init RMS 0.758584\n", "#FOTS# QuadFit found better minimum quadopt=(dt=163.994,rms=0.698519) vs oldopt=(dt=92.48,rms=0.710544)\n", "#GCMRL# 0 dt 163.993517 rms 0.699 7.918% neg 0 invalid 762 tFOTS 13.6960 tGradient 22.4980 tsec 37.2090\n", "#FOTS# QuadFit found better minimum quadopt=(dt=164.117,rms=0.680674) vs oldopt=(dt=92.48,rms=0.684569)\n", "#GCMRL# 1 dt 164.116959 rms 0.681 2.555% neg 0 invalid 762 tFOTS 13.5290 tGradient 22.6890 tsec 37.2140\n", "#FOTS# QuadFit found better minimum quadopt=(dt=166.748,rms=0.672556) vs oldopt=(dt=92.48,rms=0.674419)\n", "#GCMRL# 2 dt 166.748299 rms 0.673 1.193% neg 0 invalid 762 tFOTS 13.4120 tGradient 22.9490 tsec 37.3650\n", "#FOTS# QuadFit found better minimum quadopt=(dt=144.162,rms=0.668033) vs oldopt=(dt=92.48,rms=0.668858)\n", "#GCMRL# 3 dt 144.161616 rms 0.668 0.673% neg 0 invalid 762 tFOTS 13.4810 tGradient 22.1720 tsec 36.6610\n", "#FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.662801) vs oldopt=(dt=369.92,rms=0.662948)\n", "#GCMRL# 4 dt 295.936000 rms 0.663 0.783% neg 0 invalid 762 tFOTS 13.4150 tGradient 22.1260 tsec 36.5390\n", "#FOTS# QuadFit found better minimum quadopt=(dt=110.976,rms=0.659698) vs oldopt=(dt=92.48,rms=0.659772)\n", "#GCMRL# 5 dt 110.976000 rms 0.660 0.468% neg 0 invalid 762 tFOTS 14.2380 tGradient 22.1010 tsec 37.3480\n", "#FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.654475) vs oldopt=(dt=369.92,rms=0.655164)\n", "#GCMRL# 6 dt 517.888000 rms 0.654 0.792% neg 0 invalid 762 tFOTS 15.4310 tGradient 22.2300 tsec 38.7790\n", "#GCMRL# 7 dt 92.480000 rms 0.652 0.346% neg 0 invalid 762 tFOTS 14.2470 tGradient 23.8680 tsec 39.1470\n", "#GCMRL# 8 dt 1479.680000 rms 0.645 1.041% neg 0 invalid 762 tFOTS 13.5270 tGradient 22.9390 tsec 37.4660\n", "#GCMRL# 9 dt 92.480000 rms 0.643 0.305% neg 0 invalid 762 tFOTS 13.4720 tGradient 22.8350 tsec 37.3090\n", "#FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.641752) vs oldopt=(dt=369.92,rms=0.642094)\n", "#GCMRL# 10 dt 517.888000 rms 0.642 0.264% neg 0 invalid 762 tFOTS 14.2290 tGradient 22.8760 tsec 38.1260\n", "#FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.641504) vs oldopt=(dt=92.48,rms=0.641536)\n", "#GCMRL# 11 dt 129.472000 rms 0.642 0.000% neg 0 invalid 762 tFOTS 13.4430 tGradient 22.3460 tsec 36.7980\n", "#GCMRL# 12 dt 129.472000 rms 0.641 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.1880 tsec 23.2010\n", "#GCMRL# 13 dt 129.472000 rms 0.641 0.066% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.1700 tsec 23.1750\n", "#GCMRL# 14 dt 129.472000 rms 0.640 0.091% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.6310 tsec 23.6240\n", "#GCMRL# 15 dt 129.472000 rms 0.639 0.133% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.5700 tsec 23.5680\n", "#GCMRL# 16 dt 129.472000 rms 0.638 0.154% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.5020 tsec 23.4980\n", "#GCMRL# 17 dt 129.472000 rms 0.637 0.159% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.4060 tsec 23.4040\n", "#GCMRL# 18 dt 129.472000 rms 0.636 0.146% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.3760 tsec 23.3680\n", "#GCMRL# 19 dt 129.472000 rms 0.636 0.139% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.1930 tsec 23.1840\n", "#GCMRL# 20 dt 129.472000 rms 0.635 0.145% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.4080 tsec 23.4440\n", "#GCMRL# 21 dt 129.472000 rms 0.634 0.138% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.2990 tsec 23.3060\n", "#GCMRL# 22 dt 129.472000 rms 0.633 0.131% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.8600 tsec 23.8540\n", "#GCMRL# 23 dt 129.472000 rms 0.632 0.122% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.7470 tsec 23.7400\n", "#GCMRL# 24 dt 129.472000 rms 0.631 0.118% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.9250 tsec 23.9310\n", "#FOTS# QuadFit found better minimum quadopt=(dt=32.368,rms=0.631477) vs oldopt=(dt=23.12,rms=0.631477)\n", "\n", "#GCAMreg# pass 0 level1 5 level2 1 tsec 801.6 sigma 0.5\n", "l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.16 \n", "tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=no\n", "\n", "blurring input image with Gaussian with sigma=0.500...\n", "GCAMRegisterLevel(): init RMS 0.632139\n", "#FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.630971) vs oldopt=(dt=92.48,rms=0.631031)\n", "#GCMRL# 26 dt 129.472000 rms 0.631 0.185% neg 0 invalid 762 tFOTS 13.3270 tGradient 22.7840 tsec 37.1060\n", "#GCMRL# 27 dt 369.920000 rms 0.630 0.000% neg 0 invalid 762 tFOTS 13.3130 tGradient 22.9290 tsec 37.2560\n", "#GCMRL# 28 dt 369.920000 rms 0.630 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.8380 tsec 23.8180\n", "#GCMRL# 29 dt 369.920000 rms 0.630 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 23.0160 tsec 24.0200\n", "#GCMRL# 30 dt 369.920000 rms 0.630 0.053% neg 0 invalid 762 tFOTS 0.0000 tGradient 22.2670 tsec 23.2600\n", "setting smoothness cost coefficient to 0.615\n", "\n", "#GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2\n", "l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.62 \n", "tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=no\n", "\n", "blurring input image with Gaussian with sigma=2.000...\n", "GCAMRegisterLevel(): init RMS 0.638461\n", "#FOTS# QuadFit found better minimum quadopt=(dt=72.716,rms=0.633052) vs oldopt=(dt=103.68,rms=0.633761)\n", "#GCMRL# 32 dt 72.715953 rms 0.633 0.847% neg 0 invalid 762 tFOTS 13.3520 tGradient 14.0030 tsec 28.3480\n", "#FOTS# QuadFit found better minimum quadopt=(dt=217.924,rms=0.626214) vs oldopt=(dt=103.68,rms=0.627862)\n", "#GCMRL# 33 dt 217.924051 rms 0.626 1.080% neg 0 invalid 762 tFOTS 14.1830 tGradient 13.9330 tsec 29.1080\n", "#FOTS# QuadFit found better minimum quadopt=(dt=64.4384,rms=0.622) vs oldopt=(dt=25.92,rms=0.623136)\n", "#GCMRL# 34 dt 64.438356 rms 0.622 0.673% neg 0 invalid 762 tFOTS 13.3560 tGradient 13.9550 tsec 28.3080\n", "#FOTS# QuadFit found better minimum quadopt=(dt=101.517,rms=0.619487) vs oldopt=(dt=103.68,rms=0.619489)\n", "#GCMRL# 35 dt 101.517241 rms 0.619 0.404% neg 0 invalid 762 tFOTS 13.4030 tGradient 13.9100 tsec 28.3100\n", "#FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.618122) vs oldopt=(dt=25.92,rms=0.618385)\n", "#GCMRL# 36 dt 36.288000 rms 0.618 0.000% neg 0 invalid 762 tFOTS 13.3780 tGradient 13.9190 tsec 28.3170\n", "#GCMRL# 37 dt 36.288000 rms 0.617 0.101% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.8240 tsec 14.8140\n", "#GCMRL# 38 dt 36.288000 rms 0.616 0.168% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.8390 tsec 14.8340\n", "#GCMRL# 39 dt 36.288000 rms 0.615 0.233% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.8670 tsec 14.8660\n", "#GCMRL# 40 dt 36.288000 rms 0.613 0.274% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.8710 tsec 14.8720\n", "#GCMRL# 41 dt 36.288000 rms 0.612 0.285% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.9360 tsec 14.9330\n", "#GCMRL# 42 dt 36.288000 rms 0.610 0.274% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.8280 tsec 14.8320\n", "#GCMRL# 43 dt 36.288000 rms 0.608 0.287% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.8740 tsec 14.8780\n", "#GCMRL# 44 dt 36.288000 rms 0.607 0.249% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.9500 tsec 14.9430\n", "#GCMRL# 45 dt 36.288000 rms 0.605 0.211% neg 0 invalid 762 tFOTS 0.0000 tGradient 14.2620 tsec 15.2630\n", "#GCMRL# 46 dt 36.288000 rms 0.604 0.176% neg 0 invalid 762 tFOTS 0.0000 tGradient 14.0640 tsec 15.1280\n", "#GCMRL# 47 dt 36.288000 rms 0.604 0.125% neg 0 invalid 762 tFOTS 0.0000 tGradient 14.4130 tsec 15.4140\n", "#GCMRL# 48 dt 36.288000 rms 0.603 0.134% neg 0 invalid 762 tFOTS 0.0000 tGradient 14.3510 tsec 15.3360\n", "#GCMRL# 49 dt 36.288000 rms 0.602 0.126% neg 0 invalid 762 tFOTS 0.0000 tGradient 14.1020 tsec 15.0960\n", "#GCMRL# 50 dt 36.288000 rms 0.601 0.098% neg 0 invalid 762 tFOTS 0.0000 tGradient 14.2210 tsec 15.2210\n", "#GCMRL# 51 dt 36.288000 rms 0.601 0.067% neg 0 invalid 762 tFOTS 0.0000 tGradient 14.1290 tsec 15.1830\n", "#GCMRL# 52 dt 0.450000 rms 0.601 0.000% neg 0 invalid 762 tFOTS 13.4920 tGradient 14.3370 tsec 28.8460\n", "\n", "#GCAMreg# pass 0 level1 4 level2 1 tsec 419.644 sigma 0.5\n", "l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.62 \n", "tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=no\n", "\n", "blurring input image with Gaussian with sigma=0.500...\n", "GCAMRegisterLevel(): init RMS 0.60173\n", "#FOTS# QuadFit found better minimum quadopt=(dt=31.104,rms=0.600725) vs oldopt=(dt=25.92,rms=0.600734)\n", "#GCMRL# 54 dt 31.104000 rms 0.601 0.167% neg 0 invalid 762 tFOTS 13.4430 tGradient 14.1980 tsec 28.6520\n", "setting smoothness cost coefficient to 2.353\n", "\n", "#GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2\n", "l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.35 \n", "tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=no\n", "\n", "blurring input image with Gaussian with sigma=2.000...\n", "GCAMRegisterLevel(): init RMS 0.628375\n", "#GCMRL# 56 dt 0.000000 rms 0.628 0.118% neg 0 invalid 762 tFOTS 11.8090 tGradient 8.9990 tsec 21.8210\n", "\n", "#GCAMreg# pass 0 level1 3 level2 1 tsec 51.226 sigma 0.5\n", "l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.35 \n", "tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=no\n", "\n", "blurring input image with Gaussian with sigma=0.500...\n", "GCAMRegisterLevel(): init RMS 0.628375\n", "#GCMRL# 58 dt 0.500000 rms 0.628 0.120% neg 0 invalid 762 tFOTS 12.6740 tGradient 9.0310 tsec 22.7010\n", "#FOTS# QuadFit found better minimum quadopt=(dt=0.075,rms=0.627612) vs oldopt=(dt=0.125,rms=0.627613)\n", "#GCMRL# 59 dt 0.075000 rms 0.628 0.000% neg 0 invalid 762 tFOTS 12.5520 tGradient 8.9930 tsec 22.5780\n", "setting smoothness cost coefficient to 8.000\n", "\n", "#GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2\n", "l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=8.00 \n", "tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=no\n", "\n", "blurring input image with Gaussian with sigma=2.000...\n", "GCAMRegisterLevel(): init RMS 0.706275\n", "#FOTS# QuadFit found better minimum quadopt=(dt=2.36825,rms=0.68245) vs oldopt=(dt=2.88,rms=0.683533)\n", "#GCMRL# 61 dt 2.368248 rms 0.682 3.373% neg 0 invalid 762 tFOTS 12.8890 tGradient 6.0400 tsec 19.9420\n", "#FOTS# QuadFit found better minimum quadopt=(dt=1.75771,rms=0.679391) vs oldopt=(dt=2.88,rms=0.680485)\n", "#GCMRL# 62 dt 1.757709 rms 0.679 0.448% neg 0 invalid 762 tFOTS 12.7230 tGradient 6.0840 tsec 19.8080\n", "#FOTS# QuadFit found better minimum quadopt=(dt=1.42308,rms=0.678637) vs oldopt=(dt=0.72,rms=0.678831)\n", "#GCMRL# 63 dt 1.423077 rms 0.679 0.000% neg 0 invalid 762 tFOTS 12.6320 tGradient 6.0240 tsec 19.6780\n", "#GCMRL# 64 dt 1.423077 rms 0.679 0.013% neg 0 invalid 762 tFOTS 0.0000 tGradient 5.8790 tsec 6.8800\n", "\n", "#GCAMreg# pass 0 level1 2 level2 1 tsec 80.74 sigma 0.5\n", "l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=8.00 \n", "tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=no\n", "\n", "blurring input image with Gaussian with sigma=0.500...\n", "GCAMRegisterLevel(): init RMS 0.679068\n", "#FOTS# QuadFit found better minimum quadopt=(dt=0.252,rms=0.678531) vs oldopt=(dt=0.18,rms=0.678534)\n", "#GCMRL# 66 dt 0.252000 rms 0.679 0.079% neg 0 invalid 762 tFOTS 11.7920 tGradient 5.8860 tsec 18.6760\n", "#FOTS# QuadFit found better minimum quadopt=(dt=0.1875,rms=0.678516) vs oldopt=(dt=0.18,rms=0.678516)\n", "#GCMRL# 67 dt 0.187500 rms 0.679 0.000% neg 0 invalid 762 tFOTS 12.5900 tGradient 5.9090 tsec 19.5260\n", "setting smoothness cost coefficient to 20.000\n", "\n", "#GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2\n", "l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=20.00 \n", "tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=no\n", "\n", "blurring input image with Gaussian with sigma=2.000...\n", "GCAMRegisterLevel(): init RMS 0.725471\n", "#FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.724815) vs oldopt=(dt=0.08,rms=0.724842)\n", "#GCMRL# 69 dt 0.112000 rms 0.725 0.091% neg 0 invalid 762 tFOTS 12.6070 tGradient 3.3590 tsec 16.9560\n", "#FOTS# QuadFit found better minimum quadopt=(dt=0.384,rms=0.724213) vs oldopt=(dt=0.32,rms=0.724226)\n", "#GCMRL# 70 dt 0.384000 rms 0.724 0.000% neg 0 invalid 762 tFOTS 12.6220 tGradient 3.4130 tsec 17.0530\n", "#GCMRL# 71 dt 0.384000 rms 0.721 0.400% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.3640 tsec 4.4050\n", "#GCMRL# 72 dt 0.384000 rms 0.719 0.358% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.3670 tsec 4.3670\n", "#GCMRL# 73 dt 0.384000 rms 0.717 0.206% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4860 tsec 4.4880\n", "#GCMRL# 74 dt 0.384000 rms 0.716 0.224% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4300 tsec 4.4210\n", "#GCMRL# 75 dt 0.384000 rms 0.714 0.168% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4540 tsec 4.4490\n", "#GCMRL# 76 dt 0.384000 rms 0.714 -0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.3910 tsec 5.3390\n", "#FOTS# QuadFit found better minimum quadopt=(dt=0.768,rms=0.713161) vs oldopt=(dt=1.28,rms=0.713384)\n", "#GCMRL# 77 dt 0.768000 rms 0.713 0.176% neg 0 invalid 762 tFOTS 12.6280 tGradient 3.4410 tsec 17.0650\n", "#FOTS# QuadFit found better minimum quadopt=(dt=0.489247,rms=0.709572) vs oldopt=(dt=0.32,rms=0.710242)\n", "#GCMRL# 78 dt 0.489247 rms 0.710 0.503% neg 0 invalid 762 tFOTS 12.5550 tGradient 3.4020 tsec 16.9370\n", "#FOTS# QuadFit found better minimum quadopt=(dt=0.028,rms=0.709522) vs oldopt=(dt=0.02,rms=0.709528)\n", "#GCMRL# 79 dt 0.028000 rms 0.710 0.000% neg 0 invalid 762 tFOTS 12.5190 tGradient 3.3990 tsec 16.9260\n", "#GCMRL# 80 dt 0.028000 rms 0.710 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4070 tsec 4.3960\n", "\n", "#GCAMreg# pass 0 level1 1 level2 1 tsec 128.749 sigma 0.5\n", "l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=20.00 \n", "tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=no\n", "\n", "blurring input image with Gaussian with sigma=0.500...\n", "GCAMRegisterLevel(): init RMS 0.709986\n", "#FOTS# QuadFit found better minimum quadopt=(dt=0.028,rms=0.709517) vs oldopt=(dt=0.02,rms=0.709518)\n", "#GCMRL# 82 dt 0.028000 rms 0.710 0.066% neg 0 invalid 762 tFOTS 12.5690 tGradient 3.5570 tsec 17.1190\n", "resetting metric properties...\n", "setting smoothness cost coefficient to 40.000\n", "\n", "#GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2\n", "l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=40.00 \n", "tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=no\n", "\n", "blurring input image with Gaussian with sigma=2.000...\n", "GCAMRegisterLevel(): init RMS 0.682406\n", "#FOTS# QuadFit found better minimum quadopt=(dt=0.229784,rms=0.676832) vs oldopt=(dt=0.32,rms=0.677403)\n", "#GCMRL# 84 dt 0.229784 rms 0.677 0.817% neg 0 invalid 762 tFOTS 12.5000 tGradient 2.7990 tsec 16.2990\n", "#FOTS# QuadFit found better minimum quadopt=(dt=0.024,rms=0.676562) vs oldopt=(dt=0.02,rms=0.676563)\n", "#GCMRL# 85 dt 0.024000 rms 0.677 0.000% neg 0 invalid 762 tFOTS 12.5180 tGradient 2.7760 tsec 16.3040\n", "\n", "#GCAMreg# pass 0 level1 0 level2 1 tsec 43.762 sigma 0.5\n", "l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=40.00 \n", "tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=no\n", "\n", "blurring input image with Gaussian with sigma=0.500...\n", "GCAMRegisterLevel(): init RMS 0.677038\n", "#FOTS# QuadFit found better minimum quadopt=(dt=0.006,rms=0.676552) vs oldopt=(dt=0.005,rms=0.676552)\n", "#GCMRL# 87 dt 0.006000 rms 0.677 0.072% neg 0 invalid 762 tFOTS 12.6010 tGradient 2.7400 tsec 16.3440\n", "#GCMRL# 88 dt 0.050000 rms 0.677 0.000% neg 0 invalid 762 tFOTS 11.7870 tGradient 2.7630 tsec 15.5610\n", "GCAMregister done in 32.4389 min\n", "Starting GCAmapRenormalizeWithAlignment() without scales\n", "renormalizing by structure alignment....\n", "renormalizing input #0\n", "gca peak = 0.10253 (16)\n", "mri peak = 0.24309 ( 7)\n", "Left_Lateral_Ventricle (4): linear fit = 0.32 x + 0.0 (1137 voxels, overlap=0.004)\n", "Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1137 voxels, peak = 5), gca=6.4\n", "gca peak = 0.17690 (16)\n", "mri peak = 0.19113 (10)\n", "Right_Lateral_Ventricle (43): linear fit = 0.44 x + 0.0 (993 voxels, overlap=0.172)\n", "Right_Lateral_Ventricle (43): linear fit = 0.44 x + 0.0 (993 voxels, peak = 7), gca=7.0\n", "gca peak = 0.28275 (96)\n", "mri peak = 0.11886 (106)\n", "Right_Pallidum (52): linear fit = 1.10 x + 0.0 (865 voxels, overlap=0.105)\n", "Right_Pallidum (52): linear fit = 1.10 x + 0.0 (865 voxels, peak = 105), gca=105.1\n", "gca peak = 0.18948 (93)\n", "mri peak = 0.10308 (110)\n", "Left_Pallidum (13): linear fit = 1.13 x + 0.0 (790 voxels, overlap=0.030)\n", "Left_Pallidum (13): linear fit = 1.13 x + 0.0 (790 voxels, peak = 106), gca=105.6\n", "gca peak = 0.20755 (55)\n", "mri peak = 0.09290 (56)\n", "Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (737 voxels, overlap=1.000)\n", "Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (737 voxels, peak = 55), gca=55.0\n", "gca peak = 0.31831 (58)\n", "mri peak = 0.11220 (60)\n", "Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (713 voxels, overlap=0.999)\n", "Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (713 voxels, peak = 59), gca=59.4\n", "gca peak = 0.11957 (102)\n", "mri peak = 0.13750 (102)\n", "Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (61984 voxels, overlap=0.576)\n", "Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (61984 voxels, peak = 105), gca=104.5\n", "gca peak = 0.11429 (102)\n", "mri peak = 0.13708 (104)\n", "Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (64475 voxels, overlap=0.597)\n", "Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (64475 voxels, peak = 105), gca=104.5\n", "gca peak = 0.14521 (59)\n", "mri peak = 0.03230 (63)\n", "Left_Cerebral_Cortex (3): linear fit = 1.08 x + 0.0 (27092 voxels, overlap=0.559)\n", "Left_Cerebral_Cortex (3): linear fit = 1.08 x + 0.0 (27092 voxels, peak = 63), gca=63.4\n", "gca peak = 0.14336 (58)\n", "mri peak = 0.03626 (60)\n", "Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (27239 voxels, overlap=0.765)\n", "Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (27239 voxels, peak = 62), gca=62.4\n", "gca peak = 0.13305 (70)\n", "mri peak = 0.12909 (75)\n", "Right_Caudate (50): linear fit = 1.08 x + 0.0 (602 voxels, overlap=0.560)\n", "Right_Caudate (50): linear fit = 1.08 x + 0.0 (602 voxels, peak = 75), gca=75.2\n", "gca peak = 0.15761 (71)\n", "mri peak = 0.11149 (78)\n", "Left_Caudate (11): linear fit = 1.03 x + 0.0 (884 voxels, overlap=0.757)\n", "Left_Caudate (11): linear fit = 1.03 x + 0.0 (884 voxels, peak = 73), gca=73.5\n", "gca peak = 0.13537 (57)\n", "mri peak = 0.04425 (46)\n", "Left_Cerebellum_Cortex (8): linear fit = 0.86 x + 0.0 (20823 voxels, overlap=0.337)\n", "Left_Cerebellum_Cortex (8): linear fit = 0.86 x + 0.0 (20823 voxels, peak = 49), gca=48.7\n", "gca peak = 0.13487 (56)\n", "mri peak = 0.04085 (44)\n", "Right_Cerebellum_Cortex (47): linear fit = 0.82 x + 0.0 (23475 voxels, overlap=0.237)\n", "Right_Cerebellum_Cortex (47): linear fit = 0.82 x + 0.0 (23475 voxels, peak = 46), gca=46.2\n", "gca peak = 0.19040 (84)\n", "mri peak = 0.05880 (87)\n", "Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (6844 voxels, overlap=0.799)\n", "Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (6844 voxels, peak = 89), gca=89.5\n", "gca peak = 0.18871 (83)\n", "mri peak = 0.07503 (88)\n", "Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (6722 voxels, overlap=0.828)\n", "Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (6722 voxels, peak = 88), gca=87.6\n", "gca peak = 0.24248 (57)\n", "mri peak = 0.09624 (65)\n", "Left_Amygdala (18): linear fit = 1.10 x + 0.0 (430 voxels, overlap=1.007)\n", "Left_Amygdala (18): linear fit = 1.10 x + 0.0 (430 voxels, peak = 62), gca=62.4\n", "gca peak = 0.35833 (56)\n", "mri peak = 0.10251 (58)\n", "Right_Amygdala (54): linear fit = 1.04 x + 0.0 (501 voxels, overlap=0.958)\n", "Right_Amygdala (54): linear fit = 1.04 x + 0.0 (501 voxels, peak = 59), gca=58.5\n", "gca peak = 0.12897 (85)\n", "mri peak = 0.06635 (91)\n", "Left_Thalamus (10): linear fit = 1.08 x + 0.0 (5328 voxels, overlap=0.630)\n", "Left_Thalamus (10): linear fit = 1.08 x + 0.0 (5328 voxels, peak = 91), gca=91.4\n", "gca peak = 0.13127 (83)\n", "mri peak = 0.06776 (89)\n", "Right_Thalamus (49): linear fit = 1.12 x + 0.0 (4325 voxels, overlap=0.655)\n", "Right_Thalamus (49): linear fit = 1.12 x + 0.0 (4325 voxels, peak = 93), gca=92.5\n", "gca peak = 0.12974 (78)\n", "mri peak = 0.07627 (84)\n", "Left_Putamen (12): linear fit = 1.12 x + 0.0 (2361 voxels, overlap=0.481)\n", "Left_Putamen (12): linear fit = 1.12 x + 0.0 (2361 voxels, peak = 87), gca=87.0\n", "gca peak = 0.17796 (79)\n", "mri peak = 0.09075 (90)\n", "Right_Putamen (51): linear fit = 1.12 x + 0.0 (2325 voxels, overlap=0.594)\n", "Right_Putamen (51): linear fit = 1.12 x + 0.0 (2325 voxels, peak = 89), gca=88.9\n", "gca peak = 0.10999 (80)\n", "mri peak = 0.06213 (91)\n", "Brain_Stem (16): linear fit = 1.21 x + 0.0 (12102 voxels, overlap=0.417)\n", "Brain_Stem (16): linear fit = 1.21 x + 0.0 (12102 voxels, peak = 96), gca=96.4\n", "gca peak = 0.13215 (88)\n", "mri peak = 0.08770 (101)\n", "Right_VentralDC (60): linear fit = 1.21 x + 0.0 (1248 voxels, overlap=0.036)\n", "Right_VentralDC (60): linear fit = 1.21 x + 0.0 (1248 voxels, peak = 106), gca=106.0\n", "gca peak = 0.11941 (89)\n", "mri peak = 0.09670 (101)\n", "Left_VentralDC (28): linear fit = 1.18 x + 0.0 (1470 voxels, overlap=0.014)\n", "Left_VentralDC (28): linear fit = 1.18 x + 0.0 (1470 voxels, peak = 105), gca=105.5\n", "gca peak = 0.20775 (25)\n", "mri peak = 0.25000 ( 7)\n", "gca peak = 0.13297 (21)\n", "mri peak = 0.54545 ( 6)\n", "gca peak Unknown = 0.94777 ( 0)\n", "gca peak Left_Inf_Lat_Vent = 0.19087 (28)\n", "gca peak Third_Ventricle = 0.20775 (25)\n", "gca peak Fourth_Ventricle = 0.13297 (21)\n", "gca peak CSF = 0.16821 (33)\n", "gca peak Left_Accumbens_area = 0.32850 (63)\n", "gca peak Left_undetermined = 0.98480 (28)\n", "gca peak Left_vessel = 0.40887 (53)\n", "gca peak Left_choroid_plexus = 0.10898 (46)\n", "gca peak Right_Inf_Lat_Vent = 0.17798 (26)\n", "gca peak Right_Accumbens_area = 0.30137 (64)\n", "gca peak Right_vessel = 0.47828 (52)\n", "gca peak Right_choroid_plexus = 0.11612 (45)\n", "gca peak Fifth_Ventricle = 0.59466 (35)\n", "gca peak WM_hypointensities = 0.10053 (78)\n", "gca peak non_WM_hypointensities = 0.07253 (60)\n", "gca peak Optic_Chiasm = 0.25330 (73)\n", "not using caudate to estimate GM means\n", "estimating mean gm scale to be 1.05 x + 0.0\n", "estimating mean wm scale to be 1.02 x + 0.0\n", "estimating mean csf scale to be 0.42 x + 0.0\n", "Left_Pallidum too bright - rescaling by 0.961 (from 1.135) to 101.4 (was 105.6)\n", "Right_Pallidum too bright - rescaling by 0.965 (from 1.095) to 101.4 (was 105.1)\n", "saving intensity scales to talairach.label_intensities.txt\n", "GCAmapRenormalizeWithAlignment() took 4.90453 min\n", "noneg pre\n", "Starting GCAMregister()\n", "label assignment complete, 0 changed (0.00%)\n", "npasses = 1, nlevels = 6\n", "#pass# 1 of 1 ************************\n", "enabling zero nodes\n", "setting smoothness cost coefficient to 0.008\n", "\n", "#GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2\n", "l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01 \n", "tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=no\n", "\n", "blurring input image with Gaussian with sigma=2.000...\n", "GCAMRegisterLevel(): init RMS 0.6806\n", "#FOTS# QuadFit found better minimum quadopt=(dt=139.795,rms=0.668653) vs oldopt=(dt=92.48,rms=0.670174)\n", "#GCMRL# 90 dt 139.795222 rms 0.669 1.755% neg 0 invalid 762 tFOTS 14.8220 tGradient 13.0590 tsec 28.9730\n", "#FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.660309) vs oldopt=(dt=369.92,rms=0.660784)\n", "#GCMRL# 91 dt 295.936000 rms 0.660 1.248% neg 0 invalid 762 tFOTS 14.7560 tGradient 14.6300 tsec 30.4920\n", "#FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.656212) vs oldopt=(dt=92.48,rms=0.656504)\n", "#GCMRL# 92 dt 129.472000 rms 0.656 0.620% neg 0 invalid 762 tFOTS 15.6550 tGradient 14.8200 tsec 31.5930\n", "#FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.653722) vs oldopt=(dt=92.48,rms=0.654172)\n", "#GCMRL# 93 dt 129.472000 rms 0.654 0.379% neg 0 invalid 762 tFOTS 15.7150 tGradient 14.6390 tsec 31.4710\n", "#FOTS# QuadFit found better minimum quadopt=(dt=443.904,rms=0.650128) vs oldopt=(dt=369.92,rms=0.650158)\n", "#GCMRL# 94 dt 443.904000 rms 0.650 0.550% neg 0 invalid 762 tFOTS 14.9280 tGradient 15.0370 tsec 30.9620\n", "#GCMRL# 95 dt 92.480000 rms 0.647 0.487% neg 0 invalid 762 tFOTS 14.2400 tGradient 13.0390 tsec 28.2870\n", "#FOTS# QuadFit found better minimum quadopt=(dt=887.808,rms=0.641934) vs oldopt=(dt=1479.68,rms=0.643048)\n", "#GCMRL# 96 dt 887.808000 rms 0.642 0.777% neg 0 invalid 762 tFOTS 13.4050 tGradient 13.1100 tsec 27.5140\n", "#FOTS# QuadFit found better minimum quadopt=(dt=78.9173,rms=0.639691) vs oldopt=(dt=92.48,rms=0.639697)\n", "#GCMRL# 97 dt 78.917293 rms 0.640 0.349% neg 0 invalid 762 tFOTS 14.2610 tGradient 13.0730 tsec 28.3380\n", "#FOTS# QuadFit found better minimum quadopt=(dt=1183.74,rms=0.637391) vs oldopt=(dt=1479.68,rms=0.637705)\n", "#GCMRL# 98 dt 1183.744000 rms 0.637 0.359% neg 0 invalid 762 tFOTS 13.3980 tGradient 13.1270 tsec 27.5240\n", "#FOTS# QuadFit found better minimum quadopt=(dt=110.976,rms=0.634966) vs oldopt=(dt=92.48,rms=0.635015)\n", "#GCMRL# 99 dt 110.976000 rms 0.635 0.381% neg 0 invalid 762 tFOTS 14.1890 tGradient 13.1280 tsec 28.3150\n", "#FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.634523) vs oldopt=(dt=92.48,rms=0.634569)\n", "#GCMRL# 100 dt 129.472000 rms 0.635 0.070% neg 0 invalid 762 tFOTS 14.0230 tGradient 13.4050 tsec 28.4310\n", "#GCMRL# 101 dt 369.920000 rms 0.634 0.127% neg 0 invalid 762 tFOTS 14.2650 tGradient 13.2330 tsec 28.5410\n", "#FOTS# QuadFit found better minimum quadopt=(dt=73.984,rms=0.633149) vs oldopt=(dt=92.48,rms=0.633153)\n", "#GCMRL# 102 dt 73.984000 rms 0.633 0.090% neg 0 invalid 762 tFOTS 13.5180 tGradient 13.3570 tsec 27.9140\n", "#FOTS# QuadFit found better minimum quadopt=(dt=1183.74,rms=0.631797) vs oldopt=(dt=1479.68,rms=0.631966)\n", "#GCMRL# 103 dt 1183.744000 rms 0.632 0.214% neg 0 invalid 762 tFOTS 14.2520 tGradient 13.2970 tsec 28.5500\n", "#GCMRL# 104 dt 92.480000 rms 0.630 0.249% neg 0 invalid 762 tFOTS 14.3070 tGradient 13.3820 tsec 28.6850\n", "#FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.629901) vs oldopt=(dt=369.92,rms=0.62995)\n", "#GCMRL# 105 dt 295.936000 rms 0.630 0.051% neg 0 invalid 762 tFOTS 14.3750 tGradient 13.3920 tsec 28.7590\n", "#FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.629375) vs oldopt=(dt=92.48,rms=0.62943)\n", "#GCMRL# 106 dt 129.472000 rms 0.629 0.083% neg 0 invalid 762 tFOTS 13.3510 tGradient 13.1600 tsec 27.5160\n", "#FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.629167) vs oldopt=(dt=92.48,rms=0.629196)\n", "#GCMRL# 107 dt 129.472000 rms 0.629 0.000% neg 0 invalid 762 tFOTS 14.1410 tGradient 13.0200 tsec 28.1610\n", "#GCMRL# 108 dt 129.472000 rms 0.629 0.049% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.6110 tsec 14.6960\n", "#GCMRL# 109 dt 129.472000 rms 0.628 0.070% neg 0 invalid 762 tFOTS 0.0000 tGradient 14.8210 tsec 15.9210\n", "#GCMRL# 110 dt 129.472000 rms 0.628 0.092% neg 0 invalid 762 tFOTS 0.0000 tGradient 14.8700 tsec 15.9640\n", "#GCMRL# 111 dt 129.472000 rms 0.627 0.109% neg 0 invalid 762 tFOTS 0.0000 tGradient 14.7100 tsec 15.7970\n", "#GCMRL# 112 dt 129.472000 rms 0.626 0.137% neg 0 invalid 762 tFOTS 0.0000 tGradient 14.7300 tsec 15.8270\n", "#GCMRL# 113 dt 129.472000 rms 0.625 0.139% neg 0 invalid 762 tFOTS 0.0000 tGradient 14.6190 tsec 15.7290\n", "#GCMRL# 114 dt 129.472000 rms 0.624 0.148% neg 0 invalid 762 tFOTS 0.0000 tGradient 14.8830 tsec 15.9820\n", "#GCMRL# 115 dt 129.472000 rms 0.624 0.149% neg 0 invalid 762 tFOTS 0.0000 tGradient 14.8490 tsec 15.9590\n", "#GCMRL# 116 dt 129.472000 rms 0.623 0.140% neg 0 invalid 762 tFOTS 0.0000 tGradient 14.8460 tsec 15.9450\n", "#GCMRL# 117 dt 129.472000 rms 0.622 0.155% neg 0 invalid 762 tFOTS 0.0000 tGradient 15.0790 tsec 16.1770\n", "#GCMRL# 118 dt 129.472000 rms 0.621 0.150% neg 0 invalid 762 tFOTS 0.0000 tGradient 15.2130 tsec 16.3100\n", "#GCMRL# 119 dt 129.472000 rms 0.620 0.129% neg 0 invalid 762 tFOTS 0.0000 tGradient 15.0770 tsec 16.1730\n", "#GCMRL# 120 dt 129.472000 rms 0.619 0.139% neg 0 invalid 762 tFOTS 0.0000 tGradient 14.8650 tsec 15.9660\n", "#GCMRL# 121 dt 129.472000 rms 0.618 0.141% neg 0 invalid 762 tFOTS 0.0000 tGradient 14.6610 tsec 15.7740\n", "#GCMRL# 122 dt 129.472000 rms 0.617 0.135% neg 0 invalid 762 tFOTS 0.0000 tGradient 15.1100 tsec 16.2080\n", "#GCMRL# 123 dt 129.472000 rms 0.617 0.114% neg 0 invalid 762 tFOTS 0.0000 tGradient 14.7620 tsec 15.8670\n", "#GCMRL# 124 dt 129.472000 rms 0.616 0.120% neg 0 invalid 762 tFOTS 0.0000 tGradient 15.2610 tsec 16.3760\n", "#GCMRL# 125 dt 129.472000 rms 0.615 0.142% neg 0 invalid 762 tFOTS 0.0000 tGradient 14.8050 tsec 15.9100\n", "#GCMRL# 126 dt 129.472000 rms 0.614 0.137% neg 0 invalid 762 tFOTS 0.0000 tGradient 14.2690 tsec 15.2750\n", "#GCMRL# 127 dt 129.472000 rms 0.613 0.134% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.2040 tsec 14.2170\n", "#GCMRL# 128 dt 129.472000 rms 0.613 0.117% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.3650 tsec 14.3480\n", "#GCMRL# 129 dt 129.472000 rms 0.612 0.100% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.2840 tsec 14.2810\n", "#GCMRL# 130 dt 129.472000 rms 0.611 0.124% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.2730 tsec 14.2670\n", "#GCMRL# 131 dt 129.472000 rms 0.611 0.119% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.3620 tsec 14.3790\n", "#GCMRL# 132 dt 129.472000 rms 0.610 0.108% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.2590 tsec 14.2570\n", "#GCMRL# 133 dt 129.472000 rms 0.609 0.100% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.2120 tsec 14.2160\n", "#GCMRL# 134 dt 129.472000 rms 0.609 0.084% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.3370 tsec 14.3310\n", "#GCMRL# 135 dt 129.472000 rms 0.608 0.099% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.3420 tsec 14.3460\n", "#GCMRL# 136 dt 129.472000 rms 0.608 0.084% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.4430 tsec 14.5030\n", "#GCMRL# 137 dt 129.472000 rms 0.607 0.081% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.3820 tsec 14.3780\n", "#GCMRL# 138 dt 129.472000 rms 0.607 0.070% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.2960 tsec 14.3000\n", "#GCMRL# 139 dt 129.472000 rms 0.606 0.074% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.3200 tsec 14.3480\n", "#GCMRL# 140 dt 129.472000 rms 0.606 0.088% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.2420 tsec 14.2390\n", "#GCMRL# 141 dt 129.472000 rms 0.605 0.074% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.2170 tsec 14.2110\n", "#GCMRL# 142 dt 129.472000 rms 0.605 0.070% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.2630 tsec 14.2710\n", "#GCMRL# 143 dt 129.472000 rms 0.605 0.063% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.1580 tsec 14.1850\n", "#GCMRL# 144 dt 129.472000 rms 0.604 0.079% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.2950 tsec 14.2850\n", "#GCMRL# 145 dt 129.472000 rms 0.604 0.074% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.3080 tsec 14.2980\n", "#GCMRL# 146 dt 129.472000 rms 0.603 0.066% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.2280 tsec 14.2180\n", "#GCMRL# 147 dt 129.472000 rms 0.603 0.058% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.2530 tsec 14.2570\n", "#GCMRL# 148 dt 129.472000 rms 0.602 0.071% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.1600 tsec 14.1570\n", "#GCMRL# 149 dt 129.472000 rms 0.602 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.3440 tsec 14.3890\n", "#GCMRL# 150 dt 129.472000 rms 0.602 0.053% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.4260 tsec 14.4260\n", "#GCMRL# 151 dt 129.472000 rms 0.602 0.047% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.2740 tsec 14.2860\n", "#GCMRL# 152 dt 129.472000 rms 0.601 0.057% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.3730 tsec 14.3670\n", "#GCMRL# 153 dt 129.472000 rms 0.601 0.058% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.2130 tsec 14.2040\n", "#GCMRL# 154 dt 129.472000 rms 0.601 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.2950 tsec 14.2870\n", "#GCMRL# 155 dt 129.472000 rms 0.600 0.056% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.2640 tsec 14.2560\n", "#GCMRL# 156 dt 129.472000 rms 0.600 0.057% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.2290 tsec 14.2360\n", "#GCMRL# 157 dt 129.472000 rms 0.600 0.054% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.3920 tsec 14.3820\n", "#GCMRL# 158 dt 129.472000 rms 0.599 0.039% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.2910 tsec 14.2850\n", "#GCMRL# 159 dt 129.472000 rms 0.599 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.1910 tsec 14.1870\n", "#GCMRL# 160 dt 129.472000 rms 0.599 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.2700 tsec 14.2620\n", "#GCMRL# 161 dt 129.472000 rms 0.599 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.3320 tsec 14.3300\n", "#GCMRL# 162 dt 129.472000 rms 0.599 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.3740 tsec 14.3730\n", "#GCMRL# 163 dt 129.472000 rms 0.598 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.0620 tsec 14.0680\n", "#GCMRL# 164 dt 129.472000 rms 0.598 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.2460 tsec 14.2440\n", "#GCMRL# 165 dt 129.472000 rms 0.598 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.0420 tsec 14.0390\n", "#GCMRL# 166 dt 129.472000 rms 0.598 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.1530 tsec 14.1540\n", "#GCMRL# 167 dt 129.472000 rms 0.597 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.0860 tsec 14.0790\n", "#GCMRL# 168 dt 129.472000 rms 0.597 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.9830 tsec 13.9850\n", "#GCMRL# 169 dt 129.472000 rms 0.597 0.047% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.0750 tsec 14.0870\n", "#GCMRL# 170 dt 129.472000 rms 0.597 0.047% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.0930 tsec 14.0990\n", "#GCMRL# 171 dt 129.472000 rms 0.596 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.0610 tsec 14.0630\n", "#GCMRL# 172 dt 129.472000 rms 0.596 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.1940 tsec 14.1990\n", "#GCMRL# 173 dt 129.472000 rms 0.596 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.0640 tsec 14.0590\n", "#GCMRL# 174 dt 129.472000 rms 0.596 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.0200 tsec 14.0130\n", "#GCMRL# 175 dt 129.472000 rms 0.596 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.0940 tsec 14.0860\n", "#GCMRL# 176 dt 129.472000 rms 0.595 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.5890 tsec 14.6850\n", "#GCMRL# 177 dt 129.472000 rms 0.595 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 14.7080 tsec 15.8080\n", "#GCMRL# 178 dt 129.472000 rms 0.595 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 14.8930 tsec 15.9930\n", "#GCMRL# 179 dt 129.472000 rms 0.595 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 14.0850 tsec 15.0840\n", "#GCMRL# 180 dt 129.472000 rms 0.595 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.1530 tsec 14.1440\n", "#GCMRL# 181 dt 129.472000 rms 0.595 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.0840 tsec 14.0660\n", "#GCMRL# 182 dt 129.472000 rms 0.595 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.0660 tsec 14.0570\n", "#GCMRL# 183 dt 129.472000 rms 0.594 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.0950 tsec 14.0850\n", "#GCMRL# 184 dt 129.472000 rms 0.594 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.0390 tsec 14.0410\n", "#GCMRL# 185 dt 129.472000 rms 0.594 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.0670 tsec 14.0610\n", "#GCMRL# 186 dt 129.472000 rms 0.594 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.0570 tsec 14.0540\n", "#GCMRL# 187 dt 129.472000 rms 0.594 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.0980 tsec 14.1030\n", "#GCMRL# 188 dt 129.472000 rms 0.593 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.0550 tsec 14.0510\n", "#GCMRL# 189 dt 129.472000 rms 0.593 0.019% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.0750 tsec 14.0790\n", "#GCMRL# 190 dt 129.472000 rms 0.593 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.0580 tsec 14.0610\n", "#GCMRL# 191 dt 129.472000 rms 0.593 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.0190 tsec 14.0160\n", "#GCMRL# 192 dt 129.472000 rms 0.593 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.9680 tsec 13.9840\n", "#GCMRL# 193 dt 129.472000 rms 0.593 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.1630 tsec 14.1830\n", "#GCMRL# 194 dt 129.472000 rms 0.593 0.016% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.3150 tsec 14.3390\n", "#GCMRL# 195 dt 129.472000 rms 0.592 0.022% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.2640 tsec 14.2620\n", "#GCMRL# 196 dt 129.472000 rms 0.592 0.021% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.1850 tsec 14.2100\n", "#FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.592305) vs oldopt=(dt=369.92,rms=0.592314)\n", "#GCMRL# 197 dt 517.888000 rms 0.592 0.000% neg 0 invalid 762 tFOTS 14.4740 tGradient 13.1640 tsec 28.6880\n", "\n", "#GCAMreg# pass 0 level1 5 level2 1 tsec 1873.44 sigma 0.5\n", "l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01 \n", "tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=no\n", "\n", "blurring input image with Gaussian with sigma=0.500...\n", "GCAMRegisterLevel(): init RMS 0.592976\n", "#GCMRL# 199 dt 369.920000 rms 0.591 0.362% neg 0 invalid 762 tFOTS 13.4540 tGradient 13.3610 tsec 27.8210\n", "#FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.590529) vs oldopt=(dt=92.48,rms=0.590554)\n", "#GCMRL# 200 dt 129.472000 rms 0.591 0.051% neg 0 invalid 762 tFOTS 13.4470 tGradient 13.3740 tsec 27.8110\n", "#FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.590044) vs oldopt=(dt=369.92,rms=0.59011)\n", "#GCMRL# 201 dt 517.888000 rms 0.590 0.082% neg 0 invalid 762 tFOTS 14.2080 tGradient 13.3350 tsec 28.5460\n", "#FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.589824) vs oldopt=(dt=92.48,rms=0.589841)\n", "#GCMRL# 202 dt 129.472000 rms 0.590 0.000% neg 0 invalid 762 tFOTS 15.6600 tGradient 13.7650 tsec 30.5460\n", "#GCMRL# 203 dt 129.472000 rms 0.590 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 14.8330 tsec 15.9280\n", "#GCMRL# 204 dt 129.472000 rms 0.589 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 14.8210 tsec 15.9180\n", "#GCMRL# 205 dt 129.472000 rms 0.589 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 14.8560 tsec 15.9530\n", "#GCMRL# 206 dt 129.472000 rms 0.589 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 14.9420 tsec 16.0380\n", "#GCMRL# 207 dt 129.472000 rms 0.589 0.056% neg 0 invalid 762 tFOTS 0.0000 tGradient 14.8970 tsec 16.0050\n", "#GCMRL# 208 dt 129.472000 rms 0.588 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 14.6040 tsec 15.6150\n", "#GCMRL# 209 dt 129.472000 rms 0.588 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.1700 tsec 14.1670\n", "#GCMRL# 210 dt 129.472000 rms 0.588 0.021% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.1390 tsec 14.1350\n", "#GCMRL# 211 dt 129.472000 rms 0.588 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.1540 tsec 14.1620\n", "#GCMRL# 212 dt 129.472000 rms 0.588 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 14.0180 tsec 15.1280\n", "#GCMRL# 213 dt 129.472000 rms 0.588 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 15.0400 tsec 16.1360\n", "#GCMRL# 214 dt 129.472000 rms 0.587 0.012% neg 0 invalid 762 tFOTS 0.0000 tGradient 14.8910 tsec 16.0170\n", "#GCMRL# 215 dt 369.920000 rms 0.587 0.023% neg 0 invalid 762 tFOTS 16.5590 tGradient 14.9560 tsec 32.6030\n", "#FOTS# QuadFit found better minimum quadopt=(dt=32.368,rms=0.587309) vs oldopt=(dt=23.12,rms=0.587313)\n", "#GCMRL# 216 dt 32.368000 rms 0.587 0.000% neg 0 invalid 762 tFOTS 17.5530 tGradient 15.0360 tsec 33.7220\n", "#GCMRL# 217 dt 32.368000 rms 0.587 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 15.0510 tsec 16.1530\n", "#GCMRL# 218 dt 32.368000 rms 0.587 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 14.9500 tsec 16.0550\n", "setting smoothness cost coefficient to 0.031\n", "\n", "#GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2\n", "l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03 \n", "tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=no\n", "\n", "blurring input image with Gaussian with sigma=2.000...\n", "GCAMRegisterLevel(): init RMS 0.58983\n", "#FOTS# QuadFit found better minimum quadopt=(dt=156.781,rms=0.585278) vs oldopt=(dt=103.68,rms=0.585659)\n", "#GCMRL# 220 dt 156.781065 rms 0.585 0.772% neg 0 invalid 762 tFOTS 15.6760 tGradient 10.3330 tsec 27.1020\n", "#FOTS# QuadFit found better minimum quadopt=(dt=207.515,rms=0.577415) vs oldopt=(dt=103.68,rms=0.579197)\n", "#GCMRL# 221 dt 207.515152 rms 0.577 1.344% neg 0 invalid 762 tFOTS 15.6510 tGradient 10.1570 tsec 26.9130\n", "#FOTS# QuadFit found better minimum quadopt=(dt=64,rms=0.573321) vs oldopt=(dt=25.92,rms=0.574334)\n", "#GCMRL# 222 dt 64.000000 rms 0.573 0.709% neg 0 invalid 762 tFOTS 15.6170 tGradient 10.3160 tsec 27.0320\n", "#FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.570234) vs oldopt=(dt=103.68,rms=0.570602)\n", "#GCMRL# 223 dt 145.152000 rms 0.570 0.538% neg 0 invalid 762 tFOTS 14.7740 tGradient 10.1900 tsec 26.0660\n", "#FOTS# QuadFit found better minimum quadopt=(dt=62.208,rms=0.567687) vs oldopt=(dt=103.68,rms=0.568579)\n", "#GCMRL# 224 dt 62.208000 rms 0.568 0.447% neg 0 invalid 762 tFOTS 13.9180 tGradient 10.1550 tsec 25.0680\n", "#FOTS# QuadFit found better minimum quadopt=(dt=113.672,rms=0.565925) vs oldopt=(dt=103.68,rms=0.565929)\n", "#GCMRL# 225 dt 113.671642 rms 0.566 0.310% neg 0 invalid 762 tFOTS 13.7650 tGradient 8.6350 tsec 23.4980\n", "#FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.564047) vs oldopt=(dt=25.92,rms=0.564412)\n", "#GCMRL# 226 dt 36.288000 rms 0.564 0.332% neg 0 invalid 762 tFOTS 15.5940 tGradient 10.2690 tsec 26.9660\n", "#FOTS# QuadFit found better minimum quadopt=(dt=580.608,rms=0.554882) vs oldopt=(dt=414.72,rms=0.556925)\n", "#GCMRL# 227 dt 580.608000 rms 0.555 1.625% neg 0 invalid 762 tFOTS 14.6830 tGradient 10.2380 tsec 26.0170\n", "#FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.55334) vs oldopt=(dt=25.92,rms=0.553672)\n", "#GCMRL# 228 dt 36.288000 rms 0.553 0.278% neg 0 invalid 762 tFOTS 15.6610 tGradient 10.4240 tsec 27.1860\n", "#FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.551974) vs oldopt=(dt=103.68,rms=0.552189)\n", "#GCMRL# 229 dt 145.152000 rms 0.552 0.247% neg 0 invalid 762 tFOTS 15.5470 tGradient 10.2160 tsec 26.8620\n", "#FOTS# QuadFit found better minimum quadopt=(dt=77.848,rms=0.550892) vs oldopt=(dt=103.68,rms=0.550996)\n", "#GCMRL# 230 dt 77.847953 rms 0.551 0.196% neg 0 invalid 762 tFOTS 16.6410 tGradient 10.3180 tsec 28.0630\n", "#FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.550122) vs oldopt=(dt=103.68,rms=0.550172)\n", "#GCMRL# 231 dt 82.944000 rms 0.550 0.140% neg 0 invalid 762 tFOTS 15.6060 tGradient 10.3680 tsec 27.0900\n", "#FOTS# QuadFit found better minimum quadopt=(dt=79.4161,rms=0.549216) vs oldopt=(dt=103.68,rms=0.549297)\n", "#GCMRL# 232 dt 79.416058 rms 0.549 0.165% neg 0 invalid 762 tFOTS 16.6330 tGradient 10.2780 tsec 28.0130\n", "#FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.548731) vs oldopt=(dt=25.92,rms=0.548831)\n", "#GCMRL# 233 dt 36.288000 rms 0.549 0.088% neg 0 invalid 762 tFOTS 14.7610 tGradient 10.3340 tsec 26.2050\n", "#FOTS# QuadFit found better minimum quadopt=(dt=580.608,rms=0.545387) vs oldopt=(dt=414.72,rms=0.546)\n", "#GCMRL# 234 dt 580.608000 rms 0.545 0.609% neg 0 invalid 762 tFOTS 14.7620 tGradient 10.1480 tsec 25.9000\n", "#FOTS# QuadFit found better minimum quadopt=(dt=67.2593,rms=0.543626) vs oldopt=(dt=103.68,rms=0.544153)\n", "#GCMRL# 235 dt 67.259259 rms 0.544 0.323% neg 0 invalid 762 tFOTS 13.4490 tGradient 8.5980 tsec 23.0530\n", "#FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.543101) vs oldopt=(dt=103.68,rms=0.543167)\n", "#GCMRL# 236 dt 82.944000 rms 0.543 0.097% neg 0 invalid 762 tFOTS 13.2850 tGradient 8.5950 tsec 22.8790\n", "#FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.542423) vs oldopt=(dt=103.68,rms=0.542478)\n", "#GCMRL# 237 dt 82.944000 rms 0.542 0.125% neg 0 invalid 762 tFOTS 13.3650 tGradient 8.5670 tsec 22.9430\n", "#FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.542141) vs oldopt=(dt=25.92,rms=0.542193)\n", "#GCMRL# 238 dt 36.288000 rms 0.542 0.052% neg 0 invalid 762 tFOTS 13.2910 tGradient 8.5820 tsec 22.8640\n", "#GCMRL# 239 dt 1658.880000 rms 0.537 0.923% neg 0 invalid 762 tFOTS 14.8560 tGradient 8.4790 tsec 24.4270\n", "#FOTS# QuadFit found better minimum quadopt=(dt=69.8182,rms=0.534) vs oldopt=(dt=103.68,rms=0.534844)\n", "#GCMRL# 240 dt 69.818182 rms 0.534 0.584% neg 0 invalid 762 tFOTS 15.5830 tGradient 10.3710 tsec 27.0670\n", "#FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.533615) vs oldopt=(dt=25.92,rms=0.533669)\n", "#GCMRL# 241 dt 36.288000 rms 0.534 0.072% neg 0 invalid 762 tFOTS 13.2650 tGradient 9.6690 tsec 23.9320\n", "#FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.533199) vs oldopt=(dt=103.68,rms=0.533246)\n", "#GCMRL# 242 dt 145.152000 rms 0.533 0.078% neg 0 invalid 762 tFOTS 13.3350 tGradient 8.5990 tsec 22.9430\n", "#FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.532682) vs oldopt=(dt=103.68,rms=0.532732)\n", "#GCMRL# 243 dt 82.944000 rms 0.533 0.097% neg 0 invalid 762 tFOTS 13.3590 tGradient 8.5530 tsec 22.9170\n", "#FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.532493) vs oldopt=(dt=25.92,rms=0.532519)\n", "#GCMRL# 244 dt 36.288000 rms 0.532 0.000% neg 0 invalid 762 tFOTS 13.3280 tGradient 8.5500 tsec 22.8970\n", "#GCMRL# 245 dt 36.288000 rms 0.532 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5260 tsec 9.5170\n", "#GCMRL# 246 dt 36.288000 rms 0.532 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5440 tsec 9.5420\n", "#GCMRL# 247 dt 36.288000 rms 0.532 0.053% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.4200 tsec 9.4070\n", "#GCMRL# 248 dt 36.288000 rms 0.532 0.069% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5310 tsec 9.5330\n", "#GCMRL# 249 dt 36.288000 rms 0.531 0.079% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5550 tsec 9.5630\n", "#GCMRL# 250 dt 36.288000 rms 0.531 0.081% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.4930 tsec 9.4930\n", "#GCMRL# 251 dt 36.288000 rms 0.530 0.074% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.7910 tsec 9.9070\n", "#GCMRL# 252 dt 36.288000 rms 0.530 0.082% neg 0 invalid 762 tFOTS 0.0000 tGradient 10.1680 tsec 11.2670\n", "#GCMRL# 253 dt 36.288000 rms 0.529 0.094% neg 0 invalid 762 tFOTS 0.0000 tGradient 10.3300 tsec 11.4460\n", "#GCMRL# 254 dt 36.288000 rms 0.529 0.118% neg 0 invalid 762 tFOTS 0.0000 tGradient 10.2430 tsec 11.3500\n", "#GCMRL# 255 dt 36.288000 rms 0.528 0.116% neg 0 invalid 762 tFOTS 0.0000 tGradient 10.1210 tsec 11.2250\n", "#GCMRL# 256 dt 36.288000 rms 0.527 0.121% neg 0 invalid 762 tFOTS 0.0000 tGradient 10.3770 tsec 11.4960\n", "#GCMRL# 257 dt 36.288000 rms 0.527 0.121% neg 0 invalid 762 tFOTS 0.0000 tGradient 10.3400 tsec 11.4420\n", "#GCMRL# 258 dt 36.288000 rms 0.526 0.106% neg 0 invalid 762 tFOTS 0.0000 tGradient 10.3380 tsec 11.4380\n", "#GCMRL# 259 dt 36.288000 rms 0.526 0.110% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.7470 tsec 10.7530\n", "#GCMRL# 260 dt 36.288000 rms 0.525 0.107% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5820 tsec 9.5800\n", "#GCMRL# 261 dt 36.288000 rms 0.525 0.108% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.6170 tsec 9.6050\n", "#GCMRL# 262 dt 36.288000 rms 0.524 0.094% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.7010 tsec 9.7000\n", "#GCMRL# 263 dt 36.288000 rms 0.524 0.088% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.6160 tsec 9.6040\n", "#GCMRL# 264 dt 36.288000 rms 0.523 0.098% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5940 tsec 9.5800\n", "#GCMRL# 265 dt 36.288000 rms 0.523 0.092% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.6160 tsec 9.6040\n", "#GCMRL# 266 dt 36.288000 rms 0.522 0.090% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5420 tsec 9.5230\n", "#GCMRL# 267 dt 36.288000 rms 0.522 0.093% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.4930 tsec 9.4740\n", "#GCMRL# 268 dt 36.288000 rms 0.521 0.096% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.6280 tsec 9.6200\n", "#GCMRL# 269 dt 36.288000 rms 0.521 0.084% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5620 tsec 9.5580\n", "#GCMRL# 270 dt 36.288000 rms 0.520 0.075% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.6820 tsec 9.6710\n", "#GCMRL# 271 dt 36.288000 rms 0.520 0.060% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5700 tsec 9.5520\n", "#GCMRL# 272 dt 36.288000 rms 0.520 0.076% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.6420 tsec 9.6340\n", "#GCMRL# 273 dt 36.288000 rms 0.519 0.083% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5180 tsec 9.5160\n", "#GCMRL# 274 dt 36.288000 rms 0.519 0.080% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5720 tsec 9.5580\n", "#GCMRL# 275 dt 36.288000 rms 0.518 0.068% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5550 tsec 9.5570\n", "#GCMRL# 276 dt 36.288000 rms 0.518 0.059% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.6930 tsec 9.6900\n", "#GCMRL# 277 dt 36.288000 rms 0.518 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.6230 tsec 9.6190\n", "#GCMRL# 278 dt 36.288000 rms 0.518 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.6480 tsec 9.6310\n", "#GCMRL# 279 dt 36.288000 rms 0.517 0.066% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5330 tsec 9.5200\n", "#GCMRL# 280 dt 36.288000 rms 0.517 0.073% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.6620 tsec 9.6510\n", "#GCMRL# 281 dt 36.288000 rms 0.517 0.058% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5970 tsec 9.5860\n", "#GCMRL# 282 dt 36.288000 rms 0.516 0.056% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.6520 tsec 9.6420\n", "#GCMRL# 283 dt 36.288000 rms 0.516 0.059% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.7060 tsec 9.7000\n", "#GCMRL# 284 dt 36.288000 rms 0.516 0.064% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.6420 tsec 9.6400\n", "#GCMRL# 285 dt 36.288000 rms 0.515 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5930 tsec 9.5870\n", "#GCMRL# 286 dt 36.288000 rms 0.515 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.6760 tsec 9.6670\n", "#GCMRL# 287 dt 36.288000 rms 0.515 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5510 tsec 9.5450\n", "#GCMRL# 288 dt 36.288000 rms 0.515 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.4990 tsec 9.4960\n", "#GCMRL# 289 dt 36.288000 rms 0.515 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.6190 tsec 9.6170\n", "#GCMRL# 290 dt 36.288000 rms 0.514 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.6100 tsec 9.5910\n", "#GCMRL# 291 dt 36.288000 rms 0.514 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5300 tsec 9.5250\n", "#GCMRL# 292 dt 36.288000 rms 0.514 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5700 tsec 9.5650\n", "#GCMRL# 293 dt 36.288000 rms 0.514 0.047% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5080 tsec 9.5100\n", "#GCMRL# 294 dt 36.288000 rms 0.514 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.6030 tsec 9.6000\n", "#GCMRL# 295 dt 36.288000 rms 0.513 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.6530 tsec 9.6450\n", "#GCMRL# 296 dt 36.288000 rms 0.513 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.6160 tsec 9.6150\n", "#GCMRL# 297 dt 36.288000 rms 0.513 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.6240 tsec 9.6130\n", "#GCMRL# 298 dt 36.288000 rms 0.513 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5710 tsec 9.5700\n", "#GCMRL# 299 dt 36.288000 rms 0.513 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.6240 tsec 9.6170\n", "#GCMRL# 300 dt 36.288000 rms 0.512 0.038% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5640 tsec 9.5580\n", "#GCMRL# 301 dt 36.288000 rms 0.512 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.6700 tsec 9.6690\n", "#GCMRL# 302 dt 36.288000 rms 0.512 0.011% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5500 tsec 9.5550\n", "#GCMRL# 303 dt 36.288000 rms 0.512 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.6650 tsec 9.6620\n", "#GCMRL# 304 dt 36.288000 rms 0.512 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5680 tsec 9.5690\n", "#GCMRL# 305 dt 36.288000 rms 0.512 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.6780 tsec 9.6790\n", "#GCMRL# 306 dt 36.288000 rms 0.512 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.6450 tsec 9.6510\n", "#GCMRL# 307 dt 36.288000 rms 0.511 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.6300 tsec 9.6190\n", "#GCMRL# 308 dt 36.288000 rms 0.511 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.6080 tsec 9.6020\n", "#GCMRL# 309 dt 36.288000 rms 0.511 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5920 tsec 9.5910\n", "#GCMRL# 310 dt 36.288000 rms 0.511 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5420 tsec 9.5330\n", "#GCMRL# 311 dt 36.288000 rms 0.511 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5310 tsec 9.5280\n", "#GCMRL# 312 dt 36.288000 rms 0.511 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.6360 tsec 9.6270\n", "#GCMRL# 313 dt 36.288000 rms 0.511 0.006% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.6270 tsec 9.6280\n", "#GCMRL# 314 dt 36.288000 rms 0.510 0.018% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.6410 tsec 9.6380\n", "#GCMRL# 315 dt 36.288000 rms 0.510 0.012% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.6160 tsec 9.6220\n", "#FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.510125) vs oldopt=(dt=103.68,rms=0.510161)\n", "#GCMRL# 316 dt 145.152000 rms 0.510 0.055% neg 0 invalid 762 tFOTS 13.3480 tGradient 8.4830 tsec 22.8430\n", "#FOTS# QuadFit found better minimum quadopt=(dt=9.072,rms=0.510125) vs oldopt=(dt=6.48,rms=0.510128)\n", "#GCMRL# 317 dt 9.072000 rms 0.510 0.000% neg 0 invalid 762 tFOTS 13.3500 tGradient 8.5390 tsec 23.8110\n", "#GCMRL# 318 dt 9.072000 rms 0.510 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5420 tsec 9.5260\n", "\n", "#GCAMreg# pass 0 level1 4 level2 1 tsec 1405.16 sigma 0.5\n", "l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03 \n", "tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=no\n", "\n", "blurring input image with Gaussian with sigma=0.500...\n", "GCAMRegisterLevel(): init RMS 0.510875\n", "#FOTS# QuadFit found better minimum quadopt=(dt=115.469,rms=0.508374) vs oldopt=(dt=103.68,rms=0.508378)\n", "#GCMRL# 320 dt 115.468531 rms 0.508 0.490% neg 0 invalid 762 tFOTS 14.1900 tGradient 8.6250 tsec 23.8200\n", "#FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.507497) vs oldopt=(dt=25.92,rms=0.507669)\n", "#GCMRL# 321 dt 36.288000 rms 0.507 0.172% neg 0 invalid 762 tFOTS 12.5590 tGradient 8.5950 tsec 22.1520\n", "#FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.506808) vs oldopt=(dt=103.68,rms=0.506945)\n", "#GCMRL# 322 dt 145.152000 rms 0.507 0.136% neg 0 invalid 762 tFOTS 13.4620 tGradient 8.5890 tsec 23.0560\n", "#FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.506307) vs oldopt=(dt=103.68,rms=0.506332)\n", "#GCMRL# 323 dt 82.944000 rms 0.506 0.099% neg 0 invalid 762 tFOTS 13.4650 tGradient 8.5990 tsec 23.0600\n", "#FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.506184) vs oldopt=(dt=25.92,rms=0.506193)\n", "#GCMRL# 324 dt 36.288000 rms 0.506 0.000% neg 0 invalid 762 tFOTS 14.2220 tGradient 8.7150 tsec 23.9580\n", "#GCMRL# 325 dt 36.288000 rms 0.506 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5690 tsec 9.5790\n", "#GCMRL# 326 dt 36.288000 rms 0.506 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5100 tsec 9.5290\n", "#GCMRL# 327 dt 36.288000 rms 0.506 0.038% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5390 tsec 9.5500\n", "#GCMRL# 328 dt 36.288000 rms 0.505 0.054% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.4710 tsec 9.4800\n", "#GCMRL# 329 dt 36.288000 rms 0.505 0.069% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.4950 tsec 9.5050\n", "#GCMRL# 330 dt 36.288000 rms 0.505 0.056% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.4840 tsec 9.4860\n", "#GCMRL# 331 dt 36.288000 rms 0.504 0.057% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.4490 tsec 9.4510\n", "#GCMRL# 332 dt 36.288000 rms 0.504 0.049% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5380 tsec 9.5430\n", "#GCMRL# 333 dt 36.288000 rms 0.504 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5480 tsec 9.5350\n", "#GCMRL# 334 dt 36.288000 rms 0.504 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5200 tsec 9.5110\n", "#GCMRL# 335 dt 36.288000 rms 0.503 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5880 tsec 9.5790\n", "#GCMRL# 336 dt 36.288000 rms 0.503 0.056% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5120 tsec 9.5060\n", "#GCMRL# 337 dt 36.288000 rms 0.503 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.4960 tsec 9.4960\n", "#GCMRL# 338 dt 36.288000 rms 0.503 0.049% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5620 tsec 9.5660\n", "#GCMRL# 339 dt 36.288000 rms 0.502 0.054% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5630 tsec 9.5570\n", "#GCMRL# 340 dt 36.288000 rms 0.502 0.055% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5670 tsec 9.5560\n", "#GCMRL# 341 dt 36.288000 rms 0.502 0.038% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5910 tsec 9.5750\n", "#GCMRL# 342 dt 36.288000 rms 0.502 0.053% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5860 tsec 9.5660\n", "#GCMRL# 343 dt 36.288000 rms 0.501 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5160 tsec 9.5050\n", "#GCMRL# 344 dt 36.288000 rms 0.501 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5080 tsec 9.5080\n", "#GCMRL# 345 dt 36.288000 rms 0.501 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5520 tsec 9.5440\n", "#GCMRL# 346 dt 36.288000 rms 0.501 0.045% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.4970 tsec 9.5000\n", "#GCMRL# 347 dt 36.288000 rms 0.501 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5170 tsec 9.5180\n", "#GCMRL# 348 dt 36.288000 rms 0.500 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5030 tsec 9.5000\n", "#GCMRL# 349 dt 36.288000 rms 0.500 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5440 tsec 9.5460\n", "#GCMRL# 350 dt 36.288000 rms 0.500 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.4700 tsec 9.4770\n", "#GCMRL# 351 dt 36.288000 rms 0.500 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5810 tsec 9.5720\n", "#GCMRL# 352 dt 36.288000 rms 0.500 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5410 tsec 9.5430\n", "#GCMRL# 353 dt 36.288000 rms 0.500 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5990 tsec 9.5880\n", "#GCMRL# 354 dt 36.288000 rms 0.500 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5170 tsec 9.5060\n", "#GCMRL# 355 dt 36.288000 rms 0.499 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.6180 tsec 9.6130\n", "#GCMRL# 356 dt 36.288000 rms 0.499 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.6410 tsec 9.6350\n", "#GCMRL# 357 dt 36.288000 rms 0.499 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.6320 tsec 9.6340\n", "#GCMRL# 358 dt 36.288000 rms 0.499 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5710 tsec 9.5580\n", "#GCMRL# 359 dt 36.288000 rms 0.499 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5530 tsec 9.5460\n", "#GCMRL# 360 dt 36.288000 rms 0.499 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.6700 tsec 9.6750\n", "#GCMRL# 361 dt 36.288000 rms 0.499 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.6320 tsec 9.6500\n", "#GCMRL# 362 dt 36.288000 rms 0.498 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.6400 tsec 9.6740\n", "#GCMRL# 363 dt 36.288000 rms 0.498 0.018% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.6950 tsec 9.7150\n", "#FOTS# QuadFit found better minimum quadopt=(dt=62.208,rms=0.498249) vs oldopt=(dt=103.68,rms=0.498259)\n", "#GCMRL# 364 dt 62.208000 rms 0.498 0.000% neg 0 invalid 762 tFOTS 13.4550 tGradient 8.6730 tsec 23.1350\n", "#GCMRL# 365 dt 62.208000 rms 0.498 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.7330 tsec 9.8480\n", "#GCMRL# 366 dt 62.208000 rms 0.498 0.007% neg 0 invalid 762 tFOTS 0.0000 tGradient 10.2120 tsec 11.3230\n", "#GCMRL# 367 dt 62.208000 rms 0.498 0.018% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.8620 tsec 10.8600\n", "setting smoothness cost coefficient to 0.118\n", "\n", "#GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2\n", "l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12 \n", "tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=no\n", "\n", "blurring input image with Gaussian with sigma=2.000...\n", "GCAMRegisterLevel(): init RMS 0.509209\n", "#FOTS# QuadFit found better minimum quadopt=(dt=23,rms=0.507552) vs oldopt=(dt=32,rms=0.50775)\n", "#GCMRL# 369 dt 23.000000 rms 0.508 0.325% neg 0 invalid 762 tFOTS 13.3260 tGradient 6.3580 tsec 20.6960\n", "#FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.506084) vs oldopt=(dt=32,rms=0.506238)\n", "#GCMRL# 370 dt 44.800000 rms 0.506 0.289% neg 0 invalid 762 tFOTS 12.6350 tGradient 6.3110 tsec 19.9490\n", "#FOTS# QuadFit found better minimum quadopt=(dt=94.6087,rms=0.503948) vs oldopt=(dt=32,rms=0.50453)\n", "#GCMRL# 371 dt 94.608696 rms 0.504 0.422% neg 0 invalid 762 tFOTS 13.4950 tGradient 6.4020 tsec 20.9390\n", "#FOTS# QuadFit found better minimum quadopt=(dt=35.2711,rms=0.500346) vs oldopt=(dt=32,rms=0.500346)\n", "#GCMRL# 372 dt 35.271111 rms 0.500 0.715% neg 0 invalid 762 tFOTS 12.7110 tGradient 6.4880 tsec 20.2070\n", "#FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.498996) vs oldopt=(dt=32,rms=0.499012)\n", "#GCMRL# 373 dt 38.400000 rms 0.499 0.270% neg 0 invalid 762 tFOTS 12.6120 tGradient 6.3770 tsec 19.9840\n", "#FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.497041) vs oldopt=(dt=32,rms=0.497145)\n", "#GCMRL# 374 dt 38.400000 rms 0.497 0.392% neg 0 invalid 762 tFOTS 12.5990 tGradient 6.3060 tsec 19.9170\n", "#FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.496371) vs oldopt=(dt=32,rms=0.496441)\n", "#GCMRL# 375 dt 25.600000 rms 0.496 0.135% neg 0 invalid 762 tFOTS 12.6790 tGradient 6.2870 tsec 19.9750\n", "#FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.49469) vs oldopt=(dt=32,rms=0.495015)\n", "#GCMRL# 376 dt 44.800000 rms 0.495 0.339% neg 0 invalid 762 tFOTS 12.5870 tGradient 6.3210 tsec 19.8960\n", "#FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.494218) vs oldopt=(dt=32,rms=0.494242)\n", "#GCMRL# 377 dt 25.600000 rms 0.494 0.095% neg 0 invalid 762 tFOTS 12.6600 tGradient 6.3310 tsec 19.9840\n", "#FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.49293) vs oldopt=(dt=32,rms=0.493188)\n", "#GCMRL# 378 dt 44.800000 rms 0.493 0.261% neg 0 invalid 762 tFOTS 12.5920 tGradient 6.2990 tsec 19.9000\n", "#FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.492541) vs oldopt=(dt=32,rms=0.492576)\n", "#GCMRL# 379 dt 25.600000 rms 0.493 0.079% neg 0 invalid 762 tFOTS 12.6880 tGradient 6.3130 tsec 20.0090\n", "#FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.491364) vs oldopt=(dt=32,rms=0.491524)\n", "#GCMRL# 380 dt 44.800000 rms 0.491 0.239% neg 0 invalid 762 tFOTS 13.4540 tGradient 6.3320 tsec 20.7800\n", "#FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.491054) vs oldopt=(dt=8,rms=0.491117)\n", "#GCMRL# 381 dt 11.200000 rms 0.491 0.063% neg 0 invalid 762 tFOTS 12.5800 tGradient 6.2720 tsec 19.8480\n", "#FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.490527) vs oldopt=(dt=32,rms=0.490592)\n", "#GCMRL# 382 dt 44.800000 rms 0.491 0.107% neg 0 invalid 762 tFOTS 12.6480 tGradient 6.3150 tsec 19.9680\n", "#FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.489446) vs oldopt=(dt=32,rms=0.489571)\n", "#GCMRL# 383 dt 44.800000 rms 0.489 0.221% neg 0 invalid 762 tFOTS 13.4660 tGradient 6.2830 tsec 20.7640\n", "#FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.489184) vs oldopt=(dt=8,rms=0.489243)\n", "#GCMRL# 384 dt 11.200000 rms 0.489 0.053% neg 0 invalid 762 tFOTS 12.6160 tGradient 6.2450 tsec 19.8580\n", "#FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.488658) vs oldopt=(dt=32,rms=0.48874)\n", "#GCMRL# 385 dt 44.800000 rms 0.489 0.108% neg 0 invalid 762 tFOTS 12.6380 tGradient 6.2070 tsec 19.8450\n", "#FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.487978) vs oldopt=(dt=32,rms=0.487989)\n", "#GCMRL# 386 dt 38.400000 rms 0.488 0.139% neg 0 invalid 762 tFOTS 13.3890 tGradient 6.2840 tsec 20.6820\n", "#FOTS# QuadFit found better minimum quadopt=(dt=19.2,rms=0.487699) vs oldopt=(dt=32,rms=0.487782)\n", "#GCMRL# 387 dt 19.200000 rms 0.488 0.057% neg 0 invalid 762 tFOTS 12.6100 tGradient 6.1790 tsec 19.7910\n", "#FOTS# QuadFit found better minimum quadopt=(dt=409.6,rms=0.485709) vs oldopt=(dt=512,rms=0.485764)\n", "#GCMRL# 388 dt 409.600000 rms 0.486 0.408% neg 0 invalid 762 tFOTS 13.4830 tGradient 6.1350 tsec 20.6120\n", "#GCMRL# 389 dt 32.000000 rms 0.484 0.317% neg 0 invalid 762 tFOTS 12.6890 tGradient 6.6490 tsec 20.3420\n", "#FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.483185) vs oldopt=(dt=32,rms=0.483254)\n", "#GCMRL# 390 dt 38.400000 rms 0.483 0.204% neg 0 invalid 762 tFOTS 13.3880 tGradient 6.4900 tsec 20.8720\n", "#FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.482337) vs oldopt=(dt=32,rms=0.482434)\n", "#GCMRL# 391 dt 44.800000 rms 0.482 0.176% neg 0 invalid 762 tFOTS 12.6820 tGradient 6.1370 tsec 19.8130\n", "#FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.481884) vs oldopt=(dt=32,rms=0.481886)\n", "#GCMRL# 392 dt 25.600000 rms 0.482 0.094% neg 0 invalid 762 tFOTS 12.6640 tGradient 6.4310 tsec 20.0970\n", "#FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.481628) vs oldopt=(dt=32,rms=0.481662)\n", "#GCMRL# 393 dt 44.800000 rms 0.482 0.053% neg 0 invalid 762 tFOTS 12.5780 tGradient 6.1320 tsec 19.6980\n", "#GCMRL# 394 dt 32.000000 rms 0.481 0.053% neg 0 invalid 762 tFOTS 13.3970 tGradient 6.1500 tsec 20.5400\n", "#FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.481192) vs oldopt=(dt=32,rms=0.481214)\n", "#GCMRL# 395 dt 25.600000 rms 0.481 0.000% neg 0 invalid 762 tFOTS 13.3880 tGradient 6.1770 tsec 20.5780\n", "#GCMRL# 396 dt 25.600000 rms 0.481 0.015% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.3720 tsec 7.3700\n", "#GCMRL# 397 dt 25.600000 rms 0.481 0.073% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.1420 tsec 7.1380\n", "#GCMRL# 398 dt 25.600000 rms 0.480 0.098% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.1560 tsec 7.1500\n", "#GCMRL# 399 dt 25.600000 rms 0.480 0.081% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.1920 tsec 7.1800\n", "#GCMRL# 400 dt 25.600000 rms 0.479 0.108% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.2330 tsec 7.2310\n", "#GCMRL# 401 dt 25.600000 rms 0.479 0.116% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.4780 tsec 7.4790\n", "#GCMRL# 402 dt 25.600000 rms 0.478 0.131% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.2340 tsec 7.2290\n", "#GCMRL# 403 dt 25.600000 rms 0.477 0.155% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.1760 tsec 7.1880\n", "#GCMRL# 404 dt 25.600000 rms 0.477 0.112% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.2580 tsec 7.2620\n", "#GCMRL# 405 dt 25.600000 rms 0.476 0.146% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.4250 tsec 7.4210\n", "#GCMRL# 406 dt 25.600000 rms 0.476 0.091% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.3020 tsec 7.3060\n", "#GCMRL# 407 dt 25.600000 rms 0.475 0.081% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.2750 tsec 7.2710\n", "#GCMRL# 408 dt 25.600000 rms 0.475 0.115% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.2220 tsec 7.2250\n", "#GCMRL# 409 dt 25.600000 rms 0.474 0.142% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.2150 tsec 7.2070\n", "#GCMRL# 410 dt 25.600000 rms 0.474 0.130% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.0530 tsec 7.0580\n", "#GCMRL# 411 dt 25.600000 rms 0.473 0.087% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.1050 tsec 7.1070\n", "#GCMRL# 412 dt 25.600000 rms 0.473 -0.021% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.3570 tsec 8.2920\n", "#FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.473133) vs oldopt=(dt=8,rms=0.47314)\n", "#GCMRL# 413 dt 11.200000 rms 0.473 0.009% neg 0 invalid 762 tFOTS 13.4040 tGradient 6.3660 tsec 20.7670\n", "#GCMRL# 414 dt 32.000000 rms 0.473 0.029% neg 0 invalid 762 tFOTS 12.5730 tGradient 6.2210 tsec 19.7840\n", "#FOTS# QuadFit found better minimum quadopt=(dt=19.2,rms=0.472969) vs oldopt=(dt=32,rms=0.472976)\n", "\n", "#GCAMreg# pass 0 level1 3 level2 1 tsec 742.447 sigma 0.5\n", "l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12 \n", "tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=no\n", "\n", "blurring input image with Gaussian with sigma=0.500...\n", "GCAMRegisterLevel(): init RMS 0.473628\n", "#FOTS# QuadFit found better minimum quadopt=(dt=80.8989,rms=0.469444) vs oldopt=(dt=32,rms=0.470339)\n", "#GCMRL# 416 dt 80.898876 rms 0.469 0.883% neg 0 invalid 762 tFOTS 15.6300 tGradient 7.8800 tsec 24.6220\n", "#FOTS# QuadFit found better minimum quadopt=(dt=24.1717,rms=0.468538) vs oldopt=(dt=32,rms=0.46869)\n", "#GCMRL# 417 dt 24.171674 rms 0.469 0.193% neg 0 invalid 762 tFOTS 14.7480 tGradient 7.7850 tsec 23.6390\n", "#FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.468213) vs oldopt=(dt=32,rms=0.468216)\n", "#GCMRL# 418 dt 38.400000 rms 0.468 0.069% neg 0 invalid 762 tFOTS 14.7020 tGradient 7.7630 tsec 23.5750\n", "#FOTS# QuadFit found better minimum quadopt=(dt=19.2,rms=0.468077) vs oldopt=(dt=32,rms=0.468108)\n", "#GCMRL# 419 dt 19.200000 rms 0.468 0.000% neg 0 invalid 762 tFOTS 14.7840 tGradient 7.8010 tsec 23.7270\n", "#GCMRL# 420 dt 19.200000 rms 0.468 0.066% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7330 tsec 8.8450\n", "#GCMRL# 421 dt 19.200000 rms 0.468 0.055% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.9000 tsec 9.0160\n", "#GCMRL# 422 dt 19.200000 rms 0.467 0.076% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.9650 tsec 9.0730\n", "#GCMRL# 423 dt 19.200000 rms 0.467 0.053% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.9330 tsec 9.0600\n", "#GCMRL# 424 dt 19.200000 rms 0.467 0.086% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7690 tsec 8.8720\n", "#GCMRL# 425 dt 19.200000 rms 0.466 0.081% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.6840 tsec 8.7920\n", "#GCMRL# 426 dt 19.200000 rms 0.466 0.068% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7640 tsec 8.8690\n", "#GCMRL# 427 dt 19.200000 rms 0.466 0.064% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7910 tsec 8.8950\n", "#GCMRL# 428 dt 19.200000 rms 0.465 0.080% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7430 tsec 8.8580\n", "#GCMRL# 429 dt 19.200000 rms 0.465 0.065% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7860 tsec 8.9100\n", "#GCMRL# 430 dt 19.200000 rms 0.465 0.059% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7290 tsec 8.8380\n", "#GCMRL# 431 dt 19.200000 rms 0.464 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.6370 tsec 8.7530\n", "#GCMRL# 432 dt 19.200000 rms 0.464 0.063% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7550 tsec 8.8720\n", "#GCMRL# 433 dt 19.200000 rms 0.464 0.053% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.8360 tsec 8.9490\n", "#GCMRL# 434 dt 19.200000 rms 0.464 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.0030 tsec 9.1110\n", "#GCMRL# 435 dt 19.200000 rms 0.463 0.064% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.9160 tsec 9.0310\n", "#GCMRL# 436 dt 19.200000 rms 0.463 0.045% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.8200 tsec 8.9330\n", "#GCMRL# 437 dt 19.200000 rms 0.463 0.018% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.9250 tsec 9.0430\n", "#GCMRL# 438 dt 19.200000 rms 0.463 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.5630 tsec 8.6760\n", "#GCMRL# 439 dt 19.200000 rms 0.463 0.060% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7170 tsec 8.8210\n", "#GCMRL# 440 dt 19.200000 rms 0.463 0.005% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.6670 tsec 8.7690\n", "#GCMRL# 441 dt 19.200000 rms 0.462 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.8000 tsec 8.8990\n", "#GCMRL# 442 dt 19.200000 rms 0.462 0.055% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.8120 tsec 8.9080\n", "#GCMRL# 443 dt 19.200000 rms 0.462 -0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7960 tsec 9.9450\n", "#FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.462012) vs oldopt=(dt=32,rms=0.462015)\n", "#GCMRL# 444 dt 38.400000 rms 0.462 0.023% neg 0 invalid 762 tFOTS 14.7400 tGradient 7.7910 tsec 23.6270\n", "#FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.461955) vs oldopt=(dt=8,rms=0.46197)\n", "setting smoothness cost coefficient to 0.400\n", "\n", "#GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2\n", "l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40 \n", "tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=no\n", "\n", "blurring input image with Gaussian with sigma=2.000...\n", "GCAMRegisterLevel(): init RMS 0.485295\n", "#GCMRL# 446 dt 0.000000 rms 0.485 0.128% neg 0 invalid 762 tFOTS 14.7530 tGradient 6.2980 tsec 22.1560\n", "#GCMRL# 447 dt 0.150000 rms 0.485 0.000% neg 0 invalid 762 tFOTS 14.8050 tGradient 6.2990 tsec 23.2580\n", "\n", "#GCAMreg# pass 0 level1 2 level2 1 tsec 63.552 sigma 0.5\n", "l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40 \n", "tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=no\n", "\n", "blurring input image with Gaussian with sigma=0.500...\n", "GCAMRegisterLevel(): init RMS 0.485295\n", "#GCMRL# 449 dt 0.000000 rms 0.485 0.128% neg 0 invalid 762 tFOTS 14.7400 tGradient 6.2830 tsec 22.1230\n", "#GCMRL# 450 dt 0.150000 rms 0.485 0.000% neg 0 invalid 762 tFOTS 14.7800 tGradient 6.2950 tsec 23.2270\n", "setting smoothness cost coefficient to 1.000\n", "\n", "#GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2\n", "l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00 \n", "tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=no\n", "\n", "blurring input image with Gaussian with sigma=2.000...\n", "GCAMRegisterLevel(): init RMS 0.530295\n", "#GCMRL# 452 dt 1.280000 rms 0.527 0.634% neg 0 invalid 762 tFOTS 14.7650 tGradient 4.7540 tsec 20.6330\n", "#FOTS# QuadFit found better minimum quadopt=(dt=0.064,rms=0.526903) vs oldopt=(dt=0.08,rms=0.526903)\n", "#GCMRL# 453 dt 0.064000 rms 0.527 0.000% neg 0 invalid 762 tFOTS 14.8510 tGradient 4.7980 tsec 20.7810\n", "\n", "#GCAMreg# pass 0 level1 1 level2 1 tsec 58.174 sigma 0.5\n", "l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00 \n", "tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=no\n", "\n", "blurring input image with Gaussian with sigma=0.500...\n", "GCAMRegisterLevel(): init RMS 0.527486\n", "#FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.526684) vs oldopt=(dt=0.32,rms=0.526705)\n", "#GCMRL# 455 dt 0.448000 rms 0.527 0.152% neg 0 invalid 762 tFOTS 14.7500 tGradient 4.9010 tsec 20.7720\n", "#GCMRL# 456 dt 0.080000 rms 0.527 0.000% neg 0 invalid 762 tFOTS 14.8190 tGradient 4.8630 tsec 20.8110\n", "#GCMRL# 457 dt 0.080000 rms 0.527 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.8390 tsec 5.9600\n", "resetting metric properties...\n", "setting smoothness cost coefficient to 2.000\n", "\n", "#GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2\n", "l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00 \n", "tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=no\n", "\n", "blurring input image with Gaussian with sigma=2.000...\n", "GCAMRegisterLevel(): init RMS 0.470002\n", "#FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.456551) vs oldopt=(dt=0.32,rms=0.46005)\n", "#GCMRL# 459 dt 0.448000 rms 0.457 2.862% neg 0 invalid 762 tFOTS 13.9000 tGradient 3.4080 tsec 18.4340\n", "#FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.454157) vs oldopt=(dt=0.32,rms=0.45483)\n", "#GCMRL# 460 dt 0.448000 rms 0.454 0.524% neg 0 invalid 762 tFOTS 13.8370 tGradient 3.4540 tsec 18.4020\n", "#FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.452642) vs oldopt=(dt=0.32,rms=0.453058)\n", "#GCMRL# 461 dt 0.448000 rms 0.453 0.334% neg 0 invalid 762 tFOTS 11.8200 tGradient 2.9670 tsec 15.7930\n", "#FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.45174) vs oldopt=(dt=0.32,rms=0.451997)\n", "#GCMRL# 462 dt 0.448000 rms 0.452 0.199% neg 0 invalid 762 tFOTS 11.8500 tGradient 2.6680 tsec 15.5200\n", "#FOTS# QuadFit found better minimum quadopt=(dt=0.458333,rms=0.45102) vs oldopt=(dt=0.32,rms=0.45123)\n", "#GCMRL# 463 dt 0.458333 rms 0.451 0.159% neg 0 invalid 762 tFOTS 11.8260 tGradient 2.6800 tsec 15.5060\n", "#FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.450522) vs oldopt=(dt=0.32,rms=0.450659)\n", "#GCMRL# 464 dt 0.448000 rms 0.451 0.111% neg 0 invalid 762 tFOTS 11.8470 tGradient 2.7640 tsec 15.6040\n", "#FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.450085) vs oldopt=(dt=0.32,rms=0.450201)\n", "#GCMRL# 465 dt 0.448000 rms 0.450 0.097% neg 0 invalid 762 tFOTS 11.7900 tGradient 2.6500 tsec 15.4330\n", "#FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.449786) vs oldopt=(dt=0.32,rms=0.44987)\n", "#GCMRL# 466 dt 0.448000 rms 0.450 0.066% neg 0 invalid 762 tFOTS 11.7750 tGradient 2.7600 tsec 15.5330\n", "#FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.449478) vs oldopt=(dt=0.32,rms=0.449555)\n", "#GCMRL# 467 dt 0.448000 rms 0.449 0.068% neg 0 invalid 762 tFOTS 11.8330 tGradient 2.6700 tsec 15.5010\n", "#FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.449275) vs oldopt=(dt=0.32,rms=0.449329)\n", "#GCMRL# 468 dt 0.448000 rms 0.449 0.000% neg 0 invalid 762 tFOTS 11.8520 tGradient 2.7760 tsec 15.6610\n", "#GCMRL# 469 dt 0.448000 rms 0.449 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6460 tsec 3.6480\n", "#GCMRL# 470 dt 0.448000 rms 0.449 0.074% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7640 tsec 3.7690\n", "#GCMRL# 471 dt 0.448000 rms 0.448 0.094% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7230 tsec 3.7190\n", "#GCMRL# 472 dt 0.448000 rms 0.448 0.096% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6180 tsec 3.6170\n", "#GCMRL# 473 dt 0.448000 rms 0.447 0.085% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6550 tsec 3.6500\n", "#GCMRL# 474 dt 0.448000 rms 0.447 0.070% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6880 tsec 3.6830\n", "#GCMRL# 475 dt 0.448000 rms 0.447 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6870 tsec 3.6910\n", "#GCMRL# 476 dt 0.448000 rms 0.447 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7190 tsec 3.7360\n", "#GCMRL# 477 dt 0.448000 rms 0.447 -0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6750 tsec 5.0330\n", "#FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.446836) vs oldopt=(dt=0.08,rms=0.446836)\n", "#GCMRL# 478 dt 0.112000 rms 0.447 0.001% neg 0 invalid 762 tFOTS 11.7340 tGradient 2.7220 tsec 15.4520\n", "#FOTS# QuadFit found better minimum quadopt=(dt=0.064,rms=0.44684) vs oldopt=(dt=0.08,rms=0.44684)\n", "\n", "#GCAMreg# pass 0 level1 0 level2 1 tsec 237.373 sigma 0.5\n", "l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00 \n", "tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=no\n", "\n", "blurring input image with Gaussian with sigma=0.500...\n", "GCAMRegisterLevel(): init RMS 0.447587\n", "#FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.443597) vs oldopt=(dt=0.32,rms=0.444475)\n", "#GCMRL# 480 dt 0.448000 rms 0.444 0.891% neg 0 invalid 762 tFOTS 11.6750 tGradient 2.7090 tsec 15.3690\n", "#FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.443144) vs oldopt=(dt=0.32,rms=0.443265)\n", "#GCMRL# 481 dt 0.448000 rms 0.443 0.102% neg 0 invalid 762 tFOTS 11.7260 tGradient 2.6500 tsec 15.3640\n", "#FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.442984) vs oldopt=(dt=0.32,rms=0.443023)\n", "#GCMRL# 482 dt 0.448000 rms 0.443 0.000% neg 0 invalid 762 tFOTS 11.7060 tGradient 2.6190 tsec 15.3370\n", "#GCMRL# 483 dt 0.448000 rms 0.443 0.006% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6390 tsec 3.6380\n", "#GCMRL# 484 dt 0.448000 rms 0.443 0.018% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7150 tsec 3.7200\n", "#GCMRL# 485 dt 0.448000 rms 0.443 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.6730 tsec 4.0920\n", "GCAMregister done in 98.3608 min\n", "********************* ALLOWING NEGATIVE NODES IN DEFORMATION********************************\n", "noneg post\n", "Starting GCAMregister()\n", "label assignment complete, 0 changed (0.00%)\n", "npasses = 1, nlevels = 6\n", "#pass# 1 of 1 ************************\n", "enabling zero nodes\n", "setting smoothness cost coefficient to 0.008\n", "\n", "#GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2\n", "l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01 \n", "tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=yes\n", "\n", "blurring input image with Gaussian with sigma=2.000...\n", "GCAMRegisterLevel(): init RMS 0.441636\n", "#GCMRL# 487 dt 0.000000 rms 0.441 0.164% neg 0 invalid 762 tFOTS 14.2670 tGradient 12.8830 tsec 28.1450\n", "\n", "#GCAMreg# pass 0 level1 5 level2 1 tsec 65.791 sigma 0.5\n", "l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01 \n", "tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=yes\n", "\n", "blurring input image with Gaussian with sigma=0.500...\n", "GCAMRegisterLevel(): init RMS 0.441636\n", "#FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.440537) vs oldopt=(dt=369.92,rms=0.440559)\n", "#GCMRL# 489 dt 295.936000 rms 0.441 0.249% neg 0 invalid 762 tFOTS 14.1710 tGradient 12.8790 tsec 28.0430\n", "#FOTS# QuadFit found better minimum quadopt=(dt=32.368,rms=0.440489) vs oldopt=(dt=23.12,rms=0.440497)\n", "#GCMRL# 490 dt 32.368000 rms 0.440 0.000% neg 0 invalid 762 tFOTS 14.9120 tGradient 12.9120 tsec 28.8390\n", "#GCMRL# 491 dt 32.368000 rms 0.440 0.007% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.8110 tsec 13.8080\n", "#GCMRL# 492 dt 32.368000 rms 0.440 0.005% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.9780 tsec 13.9780\n", "#GCMRL# 493 dt 32.368000 rms 0.440 0.007% neg 0 invalid 762 tFOTS 0.0000 tGradient 13.2270 tsec 14.3310\n", "#GCMRL# 494 dt 32.368000 rms 0.440 0.009% neg 0 invalid 762 tFOTS 0.0000 tGradient 14.5970 tsec 15.7010\n", "#GCMRL# 495 dt 32.368000 rms 0.440 0.017% neg 0 invalid 762 tFOTS 0.0000 tGradient 14.4980 tsec 15.5970\n", "#GCMRL# 496 dt 32.368000 rms 0.440 0.019% neg 0 invalid 762 tFOTS 0.0000 tGradient 14.6190 tsec 15.7320\n", "setting smoothness cost coefficient to 0.031\n", "\n", "#GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2\n", "l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03 \n", "tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=yes\n", "\n", "blurring input image with Gaussian with sigma=2.000...\n", "GCAMRegisterLevel(): init RMS 0.440894\n", "#FOTS# QuadFit found better minimum quadopt=(dt=9.072,rms=0.440119) vs oldopt=(dt=6.48,rms=0.440123)\n", "#GCMRL# 498 dt 9.072000 rms 0.440 0.176% neg 0 invalid 762 tFOTS 14.8520 tGradient 8.4590 tsec 24.3000\n", "#FOTS# QuadFit found better minimum quadopt=(dt=9.072,rms=0.440099) vs oldopt=(dt=6.48,rms=0.440104)\n", "#GCMRL# 499 dt 9.072000 rms 0.440 0.000% neg 0 invalid 762 tFOTS 14.9540 tGradient 8.4290 tsec 24.4110\n", "#GCMRL# 500 dt 9.072000 rms 0.440 0.006% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.5200 tsec 9.5280\n", "\n", "#GCAMreg# pass 0 level1 4 level2 1 tsec 77.563 sigma 0.5\n", "l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03 \n", "tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=yes\n", "\n", "blurring input image with Gaussian with sigma=0.500...\n", "GCAMRegisterLevel(): init RMS 0.440843\n", "#FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.437637) vs oldopt=(dt=103.68,rms=0.438117)\n", "iter 0, gcam->neg = 1\n", "after 0 iterations, nbhd size=0, neg = 0\n", "#GCMRL# 502 dt 145.152000 rms 0.438 0.727% neg 0 invalid 762 tFOTS 14.2710 tGradient 8.3070 tsec 24.8250\n", "#FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.437455) vs oldopt=(dt=25.92,rms=0.437473)\n", "#GCMRL# 503 dt 36.288000 rms 0.437 0.000% neg 0 invalid 762 tFOTS 14.2440 tGradient 8.3150 tsec 23.5790\n", "#GCMRL# 504 dt 36.288000 rms 0.437 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.4490 tsec 9.4400\n", "#GCMRL# 505 dt 36.288000 rms 0.437 0.068% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.4280 tsec 9.4160\n", "#GCMRL# 506 dt 36.288000 rms 0.437 0.096% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.3380 tsec 9.3390\n", "iter 0, gcam->neg = 1\n", "after 0 iterations, nbhd size=0, neg = 0\n", "#GCMRL# 507 dt 36.288000 rms 0.436 0.128% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.3840 tsec 10.6210\n", "iter 0, gcam->neg = 1\n", "after 0 iterations, nbhd size=0, neg = 0\n", "#GCMRL# 508 dt 36.288000 rms 0.435 0.119% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.4180 tsec 10.6620\n", "#GCMRL# 509 dt 36.288000 rms 0.435 0.123% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.3590 tsec 9.3500\n", "iter 0, gcam->neg = 2\n", "after 7 iterations, nbhd size=1, neg = 0\n", "#GCMRL# 510 dt 36.288000 rms 0.435 0.093% neg 0 invalid 762 tFOTS 0.0000 tGradient 8.4250 tsec 14.7140\n", "#FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.434557) vs oldopt=(dt=25.92,rms=0.43456)\n", "setting smoothness cost coefficient to 0.118\n", "\n", "#GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2\n", "l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12 \n", "tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=yes\n", "\n", "blurring input image with Gaussian with sigma=2.000...\n", "GCAMRegisterLevel(): init RMS 0.435641\n", "#FOTS# QuadFit found better minimum quadopt=(dt=30.2959,rms=0.433782) vs oldopt=(dt=32,rms=0.433795)\n", "iter 0, gcam->neg = 4\n", "after 7 iterations, nbhd size=1, neg = 0\n", "#GCMRL# 512 dt 30.295858 rms 0.434 0.420% neg 0 invalid 762 tFOTS 14.9780 tGradient 6.0870 tsec 27.3030\n", "#FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.432413) vs oldopt=(dt=32,rms=0.432535)\n", "iter 0, gcam->neg = 4\n", "after 0 iterations, nbhd size=0, neg = 0\n", "#GCMRL# 513 dt 44.800000 rms 0.432 0.323% neg 0 invalid 762 tFOTS 15.0110 tGradient 5.9390 tsec 23.1790\n", "#FOTS# QuadFit found better minimum quadopt=(dt=22.2762,rms=0.431624) vs oldopt=(dt=32,rms=0.431815)\n", "#GCMRL# 514 dt 22.276243 rms 0.432 0.000% neg 0 invalid 762 tFOTS 14.9920 tGradient 6.0550 tsec 22.0560\n", "#GCMRL# 515 dt 22.276243 rms 0.431 0.138% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.0320 tsec 7.0290\n", "iter 0, gcam->neg = 2\n", "after 7 iterations, nbhd size=1, neg = 0\n", "#GCMRL# 516 dt 22.276243 rms 0.430 0.194% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.0610 tsec 12.3080\n", "#GCMRL# 517 dt 22.276243 rms 0.429 0.192% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.3680 tsec 7.3420\n", "iter 0, gcam->neg = 3\n", "after 0 iterations, nbhd size=0, neg = 0\n", "#GCMRL# 518 dt 22.276243 rms 0.429 0.199% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.0920 tsec 8.3090\n", "iter 0, gcam->neg = 1\n", "after 6 iterations, nbhd size=1, neg = 0\n", "#GCMRL# 519 dt 22.276243 rms 0.428 0.141% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.0220 tsec 11.7510\n", "iter 0, gcam->neg = 6\n", "after 10 iterations, nbhd size=1, neg = 0\n", "#GCMRL# 520 dt 22.276243 rms 0.427 0.176% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.0360 tsec 14.0540\n", "#GCMRL# 521 dt 22.276243 rms 0.427 0.143% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.0350 tsec 7.0280\n", "iter 0, gcam->neg = 6\n", "after 11 iterations, nbhd size=1, neg = 0\n", "#GCMRL# 522 dt 22.276243 rms 0.426 0.088% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.0500 tsec 14.5750\n", "iter 0, gcam->neg = 2\n", "after 2 iterations, nbhd size=0, neg = 0\n", "#GCMRL# 523 dt 22.276243 rms 0.426 0.141% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.1190 tsec 9.4860\n", "#GCMRL# 524 dt 22.276243 rms 0.425 0.130% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.0950 tsec 7.0910\n", "iter 0, gcam->neg = 1\n", "after 0 iterations, nbhd size=0, neg = 0\n", "#GCMRL# 525 dt 22.276243 rms 0.425 0.100% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.1510 tsec 8.3860\n", "iter 0, gcam->neg = 3\n", "after 8 iterations, nbhd size=1, neg = 0\n", "#GCMRL# 526 dt 22.276243 rms 0.424 0.058% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.2000 tsec 13.4850\n", "#FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.42397) vs oldopt=(dt=32,rms=0.423973)\n", "#GCMRL# 527 dt 25.600000 rms 0.424 0.089% neg 0 invalid 762 tFOTS 14.8820 tGradient 6.2230 tsec 22.0990\n", "#FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.423915) vs oldopt=(dt=8,rms=0.423917)\n", "#GCMRL# 528 dt 11.200000 rms 0.424 0.000% neg 0 invalid 762 tFOTS 14.9390 tGradient 6.0920 tsec 22.0410\n", "#GCMRL# 529 dt 11.200000 rms 0.424 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.0940 tsec 7.0900\n", "iter 0, gcam->neg = 1\n", "after 0 iterations, nbhd size=0, neg = 0\n", "#GCMRL# 530 dt 11.200000 rms 0.424 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.0800 tsec 8.3120\n", "iter 0, gcam->neg = 1\n", "after 0 iterations, nbhd size=0, neg = 0\n", "#GCMRL# 531 dt 11.200000 rms 0.424 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.0680 tsec 8.2800\n", "iter 0, gcam->neg = 1\n", "after 6 iterations, nbhd size=1, neg = 0\n", "\n", "#GCAMreg# pass 0 level1 3 level2 1 tsec 281.365 sigma 0.5\n", "l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12 \n", "tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=yes\n", "\n", "blurring input image with Gaussian with sigma=0.500...\n", "GCAMRegisterLevel(): init RMS 0.42429\n", "#FOTS# QuadFit found better minimum quadopt=(dt=66.3358,rms=0.419519) vs oldopt=(dt=32,rms=0.420377)\n", "#GCMRL# 533 dt 66.335766 rms 0.420 1.124% neg 0 invalid 762 tFOTS 17.6110 tGradient 7.2310 tsec 25.9370\n", "#FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.418766) vs oldopt=(dt=8,rms=0.418914)\n", "iter 0, gcam->neg = 1\n", "after 0 iterations, nbhd size=0, neg = 0\n", "#GCMRL# 534 dt 11.200000 rms 0.419 0.000% neg 0 invalid 762 tFOTS 17.5110 tGradient 7.6420 tsec 29.2620\n", "#GCMRL# 535 dt 11.200000 rms 0.419 0.061% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.6120 tsec 8.7240\n", "#GCMRL# 536 dt 11.200000 rms 0.418 0.057% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.5360 tsec 8.5360\n", "#GCMRL# 537 dt 11.200000 rms 0.418 0.056% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.0950 tsec 7.1160\n", "#FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.417494) vs oldopt=(dt=32,rms=0.417535)\n", "#GCMRL# 538 dt 44.800000 rms 0.417 0.129% neg 0 invalid 762 tFOTS 14.9210 tGradient 6.0900 tsec 22.0020\n", "#FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.417241) vs oldopt=(dt=8,rms=0.417279)\n", "setting smoothness cost coefficient to 0.400\n", "\n", "#GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2\n", "l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40 \n", "tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=yes\n", "\n", "blurring input image with Gaussian with sigma=2.000...\n", "GCAMRegisterLevel(): init RMS 0.423798\n", "#FOTS# QuadFit found better minimum quadopt=(dt=2.304,rms=0.422956) vs oldopt=(dt=2.88,rms=0.422956)\n", "#GCMRL# 540 dt 2.304000 rms 0.423 0.199% neg 0 invalid 762 tFOTS 15.0290 tGradient 4.8060 tsec 20.8300\n", "#FOTS# QuadFit found better minimum quadopt=(dt=1.008,rms=0.422955) vs oldopt=(dt=0.72,rms=0.422958)\n", "#GCMRL# 541 dt 1.008000 rms 0.423 0.000% neg 0 invalid 762 tFOTS 14.9530 tGradient 4.8470 tsec 20.8080\n", "#GCMRL# 542 dt 1.008000 rms 0.423 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9090 tsec 5.9000\n", "\n", "#GCAMreg# pass 0 level1 2 level2 1 tsec 63.023 sigma 0.5\n", "l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40 \n", "tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=yes\n", "\n", "blurring input image with Gaussian with sigma=0.500...\n", "GCAMRegisterLevel(): init RMS 0.423656\n", "#FOTS# QuadFit found better minimum quadopt=(dt=8.67257,rms=0.421995) vs oldopt=(dt=11.52,rms=0.422103)\n", "#GCMRL# 544 dt 8.672566 rms 0.422 0.392% neg 0 invalid 762 tFOTS 14.9780 tGradient 4.7960 tsec 20.7670\n", "#FOTS# QuadFit found better minimum quadopt=(dt=13.9429,rms=0.421202) vs oldopt=(dt=11.52,rms=0.421229)\n", "#GCMRL# 545 dt 13.942857 rms 0.421 0.000% neg 0 invalid 762 tFOTS 14.9540 tGradient 4.6860 tsec 20.6600\n", "#GCMRL# 546 dt 13.942857 rms 0.420 0.273% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.7520 tsec 5.7470\n", "iter 0, gcam->neg = 2\n", "after 0 iterations, nbhd size=0, neg = 0\n", "#GCMRL# 547 dt 13.942857 rms 0.419 0.356% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.8320 tsec 7.0470\n", "iter 0, gcam->neg = 2\n", "after 1 iterations, nbhd size=0, neg = 0\n", "#GCMRL# 548 dt 13.942857 rms 0.417 0.301% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.8880 tsec 7.6960\n", "iter 0, gcam->neg = 2\n", "after 1 iterations, nbhd size=0, neg = 0\n", "#GCMRL# 549 dt 13.942857 rms 0.415 0.468% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.8170 tsec 7.7150\n", "iter 0, gcam->neg = 2\n", "after 3 iterations, nbhd size=0, neg = 0\n", "#GCMRL# 550 dt 13.942857 rms 0.413 0.469% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.8800 tsec 8.8520\n", "iter 0, gcam->neg = 6\n", "after 9 iterations, nbhd size=1, neg = 0\n", "#GCMRL# 551 dt 13.942857 rms 0.412 0.342% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.8370 tsec 12.2790\n", "iter 0, gcam->neg = 3\n", "after 1 iterations, nbhd size=0, neg = 0\n", "#GCMRL# 552 dt 13.942857 rms 0.411 0.129% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.8110 tsec 7.6300\n", "iter 0, gcam->neg = 2\n", "after 0 iterations, nbhd size=0, neg = 0\n", "#GCMRL# 553 dt 13.942857 rms 0.411 -0.010% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.8510 tsec 8.0130\n", "#FOTS# QuadFit found better minimum quadopt=(dt=4.032,rms=0.411389) vs oldopt=(dt=2.88,rms=0.411395)\n", "iter 0, gcam->neg = 1\n", "after 0 iterations, nbhd size=0, neg = 0\n", "#GCMRL# 554 dt 4.032000 rms 0.411 0.012% neg 0 invalid 762 tFOTS 15.0030 tGradient 4.8440 tsec 22.0950\n", "#FOTS# QuadFit found better minimum quadopt=(dt=0.0016875,rms=0.411365) vs oldopt=(dt=0.0028125,rms=0.411365)\n", "setting smoothness cost coefficient to 1.000\n", "\n", "#GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2\n", "l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00 \n", "tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=yes\n", "\n", "blurring input image with Gaussian with sigma=2.000...\n", "GCAMRegisterLevel(): init RMS 0.417255\n", "#GCMRL# 556 dt 0.000000 rms 0.416 0.193% neg 0 invalid 762 tFOTS 14.3560 tGradient 3.2650 tsec 18.6190\n", "\n", "#GCAMreg# pass 0 level1 1 level2 1 tsec 46.647 sigma 0.5\n", "l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00 \n", "tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=yes\n", "\n", "blurring input image with Gaussian with sigma=0.500...\n", "GCAMRegisterLevel(): init RMS 0.417255\n", "#GCMRL# 558 dt 0.000000 rms 0.416 0.193% neg 0 invalid 762 tFOTS 14.2540 tGradient 3.2390 tsec 18.4880\n", "resetting metric properties...\n", "setting smoothness cost coefficient to 2.000\n", "\n", "#GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2\n", "l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00 \n", "tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=yes\n", "\n", "blurring input image with Gaussian with sigma=2.000...\n", "GCAMRegisterLevel(): init RMS 0.408762\n", "#FOTS# QuadFit found better minimum quadopt=(dt=1.88843,rms=0.385579) vs oldopt=(dt=1.28,rms=0.388123)\n", "iter 0, gcam->neg = 624\n", "after 13 iterations, nbhd size=1, neg = 0\n", "#GCMRL# 560 dt 1.888427 rms 0.386 5.618% neg 0 invalid 762 tFOTS 15.0570 tGradient 2.6290 tsec 27.5280\n", "#GCMRL# 561 dt 0.000013 rms 0.386 0.000% neg 0 invalid 762 tFOTS 19.8990 tGradient 2.8220 tsec 23.8520\n", "\n", "#GCAMreg# pass 0 level1 0 level2 1 tsec 65.756 sigma 0.5\n", "l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00 \n", "tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=yes\n", "\n", "blurring input image with Gaussian with sigma=0.500...\n", "GCAMRegisterLevel(): init RMS 0.386748\n", "#FOTS# QuadFit found better minimum quadopt=(dt=0.028,rms=0.385744) vs oldopt=(dt=0.02,rms=0.385752)\n", "#GCMRL# 563 dt 0.028000 rms 0.386 0.259% neg 0 invalid 762 tFOTS 17.6780 tGradient 3.4960 tsec 22.2760\n", "#FOTS# QuadFit found better minimum quadopt=(dt=0.007,rms=0.385783) vs oldopt=(dt=0.005,rms=0.385784)\n", "#GCMRL# 564 dt 0.007000 rms 0.386 0.000% neg 0 invalid 762 tFOTS 17.7370 tGradient 3.5610 tsec 23.4560\n", "#GCMRL# 565 dt 0.007000 rms 0.386 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.6010 tsec 4.7050\n", "#GCMRL# 566 dt 0.007000 rms 0.386 0.006% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4570 tsec 4.5570\n", "label assignment complete, 0 changed (0.00%)\n", "GCAMregister done in 21.6806 min\n", "Starting GCAMcomputeMaxPriorLabels()\n", "Morphing with label term set to 0 *******************************\n", "Starting GCAMregister()\n", "label assignment complete, 0 changed (0.00%)\n", "npasses = 1, nlevels = 6\n", "#pass# 1 of 1 ************************\n", "enabling zero nodes\n", "setting smoothness cost coefficient to 0.008\n", "\n", "#GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2\n", "l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.01 \n", "tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=yes\n", "\n", "blurring input image with Gaussian with sigma=2.000...\n", "GCAMRegisterLevel(): init RMS 0.375653\n", "\n", "#GCAMreg# pass 0 level1 5 level2 1 tsec 41.725 sigma 0.5\n", "l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.01 \n", "tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=yes\n", "\n", "blurring input image with Gaussian with sigma=0.500...\n", "GCAMRegisterLevel(): init RMS 0.375653\n", "#FOTS# QuadFit found better minimum quadopt=(dt=8.092,rms=0.375651) vs oldopt=(dt=5.78,rms=0.375651)\n", "#GCMRL# 569 dt 8.092000 rms 0.376 0.001% neg 0 invalid 762 tFOTS 14.6390 tGradient 13.2170 tsec 28.8410\n", "#FOTS# QuadFit found better minimum quadopt=(dt=2.023,rms=0.375651) vs oldopt=(dt=1.445,rms=0.375651)\n", "#GCMRL# 570 dt 2.023000 rms 0.376 0.000% neg 0 invalid 762 tFOTS 14.6550 tGradient 12.4410 tsec 28.1080\n", "#GCMRL# 571 dt 2.023000 rms 0.376 0.000% neg 0 invalid 762 tFOTS 0.0000 tGradient 12.5240 tsec 13.5120\n", "setting smoothness cost coefficient to 0.031\n", "\n", "#GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2\n", "l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.03 \n", "tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=yes\n", "\n", "blurring input image with Gaussian with sigma=2.000...\n", "GCAMRegisterLevel(): init RMS 0.37578\n", "#FOTS# QuadFit found better minimum quadopt=(dt=2.268,rms=0.375776) vs oldopt=(dt=1.62,rms=0.375777)\n", "#GCMRL# 573 dt 2.268000 rms 0.376 0.001% neg 0 invalid 762 tFOTS 15.5660 tGradient 7.8830 tsec 24.5310\n", "#FOTS# QuadFit found better minimum quadopt=(dt=1.944,rms=0.375775) vs oldopt=(dt=1.62,rms=0.375775)\n", "#GCMRL# 574 dt 1.944000 rms 0.376 0.000% neg 0 invalid 762 tFOTS 17.2520 tGradient 9.0320 tsec 27.3990\n", "\n", "#GCAMreg# pass 0 level1 4 level2 1 tsec 71.774 sigma 0.5\n", "l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.03 \n", "tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=yes\n", "\n", "blurring input image with Gaussian with sigma=0.500...\n", "GCAMRegisterLevel(): init RMS 0.375775\n", "#GCMRL# 576 dt 25.920000 rms 0.376 0.015% neg 0 invalid 762 tFOTS 16.2590 tGradient 9.0250 tsec 26.3680\n", "#FOTS# QuadFit found better minimum quadopt=(dt=20.8,rms=0.375706) vs oldopt=(dt=25.92,rms=0.375708)\n", "#GCMRL# 577 dt 20.800000 rms 0.376 0.000% neg 0 invalid 762 tFOTS 17.1880 tGradient 9.0380 tsec 27.3300\n", "#GCMRL# 578 dt 20.800000 rms 0.376 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 9.0090 tsec 10.0920\n", "setting smoothness cost coefficient to 0.118\n", "\n", "#GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2\n", "l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.12 \n", "tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=yes\n", "\n", "blurring input image with Gaussian with sigma=2.000...\n", "GCAMRegisterLevel(): init RMS 0.376188\n", "#FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.375971) vs oldopt=(dt=8,rms=0.375989)\n", "#GCMRL# 580 dt 11.200000 rms 0.376 0.058% neg 0 invalid 762 tFOTS 17.2790 tGradient 6.6850 tsec 25.0560\n", "#FOTS# QuadFit found better minimum quadopt=(dt=6.4,rms=0.37594) vs oldopt=(dt=8,rms=0.375943)\n", "#GCMRL# 581 dt 6.400000 rms 0.376 0.000% neg 0 invalid 762 tFOTS 17.2550 tGradient 6.7100 tsec 25.0810\n", "\n", "#GCAMreg# pass 0 level1 3 level2 1 tsec 68.697 sigma 0.5\n", "l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.12 \n", "tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=yes\n", "\n", "blurring input image with Gaussian with sigma=0.500...\n", "GCAMRegisterLevel(): init RMS 0.37594\n", "#FOTS# QuadFit found better minimum quadopt=(dt=86.9565,rms=0.374039) vs oldopt=(dt=32,rms=0.374485)\n", "iter 0, gcam->neg = 22\n", "after 9 iterations, nbhd size=1, neg = 0\n", "#GCMRL# 583 dt 86.956522 rms 0.374 0.497% neg 0 invalid 762 tFOTS 17.2580 tGradient 6.6680 tsec 40.0460\n", "#FOTS# QuadFit found better minimum quadopt=(dt=25.4316,rms=0.373277) vs oldopt=(dt=32,rms=0.373375)\n", "iter 0, gcam->neg = 7\n", "after 3 iterations, nbhd size=0, neg = 0\n", "#GCMRL# 584 dt 25.431579 rms 0.373 0.000% neg 0 invalid 762 tFOTS 17.2140 tGradient 6.6830 tsec 31.9530\n", "iter 0, gcam->neg = 1\n", "after 0 iterations, nbhd size=0, neg = 0\n", "#GCMRL# 585 dt 25.431579 rms 0.373 0.083% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.7230 tsec 10.6670\n", "iter 0, gcam->neg = 7\n", "after 2 iterations, nbhd size=0, neg = 0\n", "#GCMRL# 586 dt 25.431579 rms 0.373 0.095% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.6550 tsec 13.3030\n", "iter 0, gcam->neg = 9\n", "after 12 iterations, nbhd size=1, neg = 0\n", "#GCMRL# 587 dt 25.431579 rms 0.372 0.083% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.7120 tsec 26.9190\n", "iter 0, gcam->neg = 10\n", "after 5 iterations, nbhd size=0, neg = 0\n", "#GCMRL# 588 dt 25.431579 rms 0.372 0.108% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.6460 tsec 17.3870\n", "iter 0, gcam->neg = 15\n", "after 11 iterations, nbhd size=1, neg = 0\n", "#GCMRL# 589 dt 25.431579 rms 0.372 0.096% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.7090 tsec 25.5300\n", "#FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.371393) vs oldopt=(dt=32,rms=0.371426)\n", "iter 0, gcam->neg = 1\n", "after 0 iterations, nbhd size=0, neg = 0\n", "setting smoothness cost coefficient to 0.400\n", "\n", "#GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2\n", "l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.40 \n", "tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=yes\n", "\n", "blurring input image with Gaussian with sigma=2.000...\n", "GCAMRegisterLevel(): init RMS 0.374087\n", "#FOTS# QuadFit found better minimum quadopt=(dt=3.456,rms=0.373984) vs oldopt=(dt=2.88,rms=0.373988)\n", "#GCMRL# 591 dt 3.456000 rms 0.374 0.028% neg 0 invalid 762 tFOTS 14.6320 tGradient 4.2830 tsec 19.8870\n", "#FOTS# QuadFit found better minimum quadopt=(dt=1.008,rms=0.373976) vs oldopt=(dt=0.72,rms=0.373977)\n", "#GCMRL# 592 dt 1.008000 rms 0.374 0.000% neg 0 invalid 762 tFOTS 13.8560 tGradient 4.2860 tsec 19.1400\n", "#GCMRL# 593 dt 1.008000 rms 0.374 0.001% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3080 tsec 5.2920\n", "iter 0, gcam->neg = 1\n", "after 1 iterations, nbhd size=0, neg = 0\n", "\n", "#GCAMreg# pass 0 level1 2 level2 1 tsec 61.044 sigma 0.5\n", "l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.40 \n", "tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=yes\n", "\n", "blurring input image with Gaussian with sigma=0.500...\n", "GCAMRegisterLevel(): init RMS 0.373974\n", "#FOTS# QuadFit found better minimum quadopt=(dt=21.7358,rms=0.372501) vs oldopt=(dt=11.52,rms=0.372842)\n", "iter 0, gcam->neg = 11\n", "after 3 iterations, nbhd size=0, neg = 0\n", "#GCMRL# 595 dt 21.735849 rms 0.372 0.394% neg 0 invalid 762 tFOTS 16.2350 tGradient 4.2850 tsec 26.0320\n", "#FOTS# QuadFit found better minimum quadopt=(dt=22.8571,rms=0.37164) vs oldopt=(dt=11.52,rms=0.371845)\n", "iter 0, gcam->neg = 17\n", "after 10 iterations, nbhd size=1, neg = 0\n", "#GCMRL# 596 dt 22.857143 rms 0.372 0.000% neg 0 invalid 762 tFOTS 14.6410 tGradient 4.2500 tsec 26.9380\n", "iter 0, gcam->neg = 27\n", "after 15 iterations, nbhd size=1, neg = 0\n", "setting smoothness cost coefficient to 1.000\n", "\n", "#GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2\n", "l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=1.00 \n", "tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=yes\n", "\n", "blurring input image with Gaussian with sigma=2.000...\n", "GCAMRegisterLevel(): init RMS 0.376315\n", "#FOTS# QuadFit found better minimum quadopt=(dt=-0.000160217,rms=0.376315) vs oldopt=(dt=7.8125e-05,rms=0.376315)\n", "#GCMRL# 598 dt -0.000160 rms 0.376 0.000% neg 0 invalid 762 tFOTS 18.4170 tGradient 2.7270 tsec 22.1140\n", "\n", "#GCAMreg# pass 0 level1 1 level2 1 tsec 49.123 sigma 0.5\n", "l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=1.00 \n", "tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=yes\n", "\n", "blurring input image with Gaussian with sigma=0.500...\n", "GCAMRegisterLevel(): init RMS 0.376315\n", "resetting metric properties...\n", "setting smoothness cost coefficient to 2.000\n", "\n", "#GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2\n", "l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=2.00 \n", "tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=yes\n", "\n", "blurring input image with Gaussian with sigma=2.000...\n", "GCAMRegisterLevel(): init RMS 0.368515\n", "#FOTS# QuadFit found better minimum quadopt=(dt=1.11117,rms=0.361078) vs oldopt=(dt=1.28,rms=0.361224)\n", "iter 0, gcam->neg = 480\n", "after 16 iterations, nbhd size=1, neg = 0\n", "#GCMRL# 601 dt 1.111171 rms 0.362 1.841% neg 0 invalid 762 tFOTS 14.6090 tGradient 2.0770 tsec 28.2070\n", "#FOTS# QuadFit found better minimum quadopt=(dt=2.34375e-05,rms=0.361732) vs oldopt=(dt=1.95313e-05,rms=0.361732)\n", "#GCMRL# 602 dt 0.000023 rms 0.362 0.000% neg 0 invalid 762 tFOTS 18.3960 tGradient 2.0970 tsec 21.4880\n", "\n", "#GCAMreg# pass 0 level1 0 level2 1 tsec 62.043 sigma 0.5\n", "l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=2.00 \n", "tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=yes\n", "\n", "blurring input image with Gaussian with sigma=0.500...\n", "GCAMRegisterLevel(): init RMS 0.361732\n", "#FOTS# QuadFit found better minimum quadopt=(dt=0.064,rms=0.361659) vs oldopt=(dt=0.08,rms=0.361659)\n", "#GCMRL# 604 dt 0.064000 rms 0.362 0.020% neg 0 invalid 762 tFOTS 14.6680 tGradient 2.1200 tsec 17.7680\n", "#FOTS# QuadFit found better minimum quadopt=(dt=0.028,rms=0.361639) vs oldopt=(dt=0.02,rms=0.361643)\n", "#GCMRL# 605 dt 0.028000 rms 0.362 0.000% neg 0 invalid 762 tFOTS 14.7730 tGradient 2.0850 tsec 17.8680\n", "#GCMRL# 606 dt 0.028000 rms 0.362 0.004% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.0870 tsec 3.0680\n", "GCAMregister done in 14.3127 min\n", "writing output transformation to transforms/talairach.m3z...\n", "GCAMwrite\n", "Calls to gcamLogLikelihoodEnergy 4499 tmin = 15.7958\n", "Calls to gcamLabelEnergy 3971 tmin = 1.40543\n", "Calls to gcamJacobianEnergy 4499 tmin = 15.9149\n", "Calls to gcamSmoothnessEnergy 4499 tmin = 9.72668\n", "Calls to gcamLogLikelihoodTerm 608 tmin = 5.17678\n", "Calls to gcamLabelTerm 568 tmin = 7.171\n", "Calls to gcamJacobianTerm 608 tmin = 12.186\n", "Calls to gcamSmoothnessTerm 608 tmin = 2.22427\n", "Calls to gcamComputeGradient 608 tmin = 96.8958\n", "Calls to gcamComputeMetricProperties 6257 tmin = 17.1354\n", "mri_ca_register took 2 hours, 52 minutes and 0 seconds.\n", "#VMPC# mri_ca_register VmPeak 2023732\n", "FSRUNTIME@ mri_ca_register 2.8666 hours 1 threads\n", "#--------------------------------------\n", "#@# SubCort Seg Thu Jun 29 06:11:21 UTC 2023\n", "\n", " mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /opt/freesurfer-7.3.2/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz \n", "\n", "sysname Linux\n", "hostname jupyter-stebo85\n", "machine x86_64\n", "\n", "setenv SUBJECTS_DIR /home/jovyan/example-notebooks/structural_imaging/freesurfer_output\n", "cd /home/jovyan/example-notebooks/structural_imaging/freesurfer_output/subjectname/mri\n", "mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /opt/freesurfer-7.3.2/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz \n", "\n", "relabeling unlikely voxels with window_size = 9 and prior threshold 0.30\n", "using Gibbs prior factor = 0.500\n", "renormalizing sequences with structure alignment, equivalent to:\n", "\t-renormalize\n", "\t-renormalize_mean 0.500\n", "\t-regularize 0.500\n", "\n", "== Number of threads available to for OpenMP = 1 == \n", "reading 1 input volumes\n", "reading classifier array from /opt/freesurfer-7.3.2/average/RB_all_2020-01-02.gca\n", "reading input volume from norm.mgz\n", "average std[0] = 7.2\n", "reading transform from transforms/talairach.m3z\n", "setting orig areas to linear transform determinant scaled 6.27\n", "Atlas used for the 3D morph was /opt/freesurfer-7.3.2/average/RB_all_2020-01-02.gca\n", "average std = 7.2 using min determinant for regularization = 5.2\n", "0 singular and 0 ill-conditioned covariance matrices regularized\n", "labeling volume...\n", "renormalizing by structure alignment....\n", "renormalizing input #0\n", "gca peak = 0.15521 (20)\n", "mri peak = 0.17945 ( 7)\n", "Left_Lateral_Ventricle (4): linear fit = 0.35 x + 0.0 (1560 voxels, overlap=0.004)\n", "Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1560 voxels, peak = 7), gca=8.0\n", "gca peak = 0.20380 (13)\n", "mri peak = 0.17272 ( 7)\n", "Right_Lateral_Ventricle (43): linear fit = 0.43 x + 0.0 (1589 voxels, overlap=0.049)\n", "Right_Lateral_Ventricle (43): linear fit = 0.43 x + 0.0 (1589 voxels, peak = 6), gca=5.5\n", "gca peak = 0.26283 (96)\n", "mri peak = 0.16332 (106)\n", "Right_Pallidum (52): linear fit = 1.10 x + 0.0 (819 voxels, overlap=0.128)\n", "Right_Pallidum (52): linear fit = 1.10 x + 0.0 (819 voxels, peak = 105), gca=105.1\n", "gca peak = 0.15814 (97)\n", "mri peak = 0.11072 (106)\n", "Left_Pallidum (13): linear fit = 1.12 x + 0.0 (858 voxels, overlap=0.026)\n", "Left_Pallidum (13): linear fit = 1.12 x + 0.0 (858 voxels, peak = 109), gca=109.1\n", "gca peak = 0.27624 (56)\n", "mri peak = 0.10696 (56)\n", "Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (782 voxels, overlap=1.011)\n", "Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (782 voxels, peak = 56), gca=56.0\n", "gca peak = 0.28723 (59)\n", "mri peak = 0.09347 (60)\n", "Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (838 voxels, overlap=1.011)\n", "Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (838 voxels, peak = 60), gca=60.5\n", "gca peak = 0.07623 (103)\n", "mri peak = 0.13857 (102)\n", "Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (41973 voxels, overlap=0.615)\n", "Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (41973 voxels, peak = 103), gca=103.0\n", "gca peak = 0.07837 (105)\n", "mri peak = 0.13751 (104)\n", "Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (43265 voxels, overlap=0.620)\n", "Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (43265 voxels, peak = 105), gca=105.0\n", "gca peak = 0.10165 (58)\n", "mri peak = 0.04398 (66)\n", "Left_Cerebral_Cortex (3): linear fit = 1.10 x + 0.0 (29448 voxels, overlap=0.783)\n", "Left_Cerebral_Cortex (3): linear fit = 1.10 x + 0.0 (29448 voxels, peak = 64), gca=63.5\n", "gca peak = 0.11113 (58)\n", "mri peak = 0.04406 (64)\n", "Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (28388 voxels, overlap=0.735)\n", "Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (28388 voxels, peak = 62), gca=62.4\n", "gca peak = 0.27796 (67)\n", "mri peak = 0.18231 (76)\n", "Right_Caudate (50): linear fit = 1.12 x + 0.0 (935 voxels, overlap=0.231)\n", "Right_Caudate (50): linear fit = 1.12 x + 0.0 (935 voxels, peak = 75), gca=74.7\n", "gca peak = 0.14473 (69)\n", "mri peak = 0.13884 (77)\n", "Left_Caudate (11): linear fit = 1.00 x + 0.0 (901 voxels, overlap=0.937)\n", "Left_Caudate (11): linear fit = 1.00 x + 0.0 (901 voxels, peak = 69), gca=69.0\n", "gca peak = 0.14301 (56)\n", "mri peak = 0.05310 (48)\n", "Left_Cerebellum_Cortex (8): linear fit = 0.86 x + 0.0 (14929 voxels, overlap=0.755)\n", "Left_Cerebellum_Cortex (8): linear fit = 0.86 x + 0.0 (14929 voxels, peak = 48), gca=47.9\n", "gca peak = 0.14610 (55)\n", "mri peak = 0.04965 (46)\n", "Right_Cerebellum_Cortex (47): linear fit = 0.83 x + 0.0 (15407 voxels, overlap=0.643)\n", "Right_Cerebellum_Cortex (47): linear fit = 0.83 x + 0.0 (15407 voxels, peak = 46), gca=45.9\n", "gca peak = 0.16309 (85)\n", "mri peak = 0.07994 (89)\n", "Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (5075 voxels, overlap=0.821)\n", "Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (5075 voxels, peak = 91), gca=90.5\n", "gca peak = 0.15172 (84)\n", "mri peak = 0.08530 (88)\n", "Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (5192 voxels, overlap=0.827)\n", "Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (5192 voxels, peak = 89), gca=89.5\n", "gca peak = 0.30461 (58)\n", "mri peak = 0.10000 (63)\n", "Left_Amygdala (18): linear fit = 1.10 x + 0.0 (469 voxels, overlap=0.856)\n", "Left_Amygdala (18): linear fit = 1.10 x + 0.0 (469 voxels, peak = 64), gca=63.5\n", "gca peak = 0.32293 (57)\n", "mri peak = 0.11073 (62)\n", "Right_Amygdala (54): linear fit = 1.10 x + 0.0 (449 voxels, overlap=0.625)\n", "Right_Amygdala (54): linear fit = 1.10 x + 0.0 (449 voxels, peak = 62), gca=62.4\n", "gca peak = 0.11083 (90)\n", "mri peak = 0.08778 (91)\n", "Left_Thalamus (10): linear fit = 1.05 x + 0.0 (4105 voxels, overlap=0.842)\n", "Left_Thalamus (10): linear fit = 1.05 x + 0.0 (4105 voxels, peak = 95), gca=94.9\n", "gca peak = 0.11393 (83)\n", "mri peak = 0.08291 (89)\n", "Right_Thalamus (49): linear fit = 1.10 x + 0.0 (4093 voxels, overlap=0.697)\n", "Right_Thalamus (49): linear fit = 1.10 x + 0.0 (4093 voxels, peak = 91), gca=90.9\n", "gca peak = 0.08575 (81)\n", "mri peak = 0.09072 (84)\n", "Left_Putamen (12): linear fit = 1.10 x + 0.0 (1968 voxels, overlap=0.477)\n", "Left_Putamen (12): linear fit = 1.10 x + 0.0 (1968 voxels, peak = 89), gca=88.7\n", "gca peak = 0.08618 (78)\n", "mri peak = 0.09372 (88)\n", "Right_Putamen (51): linear fit = 1.10 x + 0.0 (2102 voxels, overlap=0.522)\n", "Right_Putamen (51): linear fit = 1.10 x + 0.0 (2102 voxels, peak = 85), gca=85.4\n", "gca peak = 0.08005 (78)\n", "mri peak = 0.06509 (96)\n", "Brain_Stem (16): linear fit = 1.18 x + 0.0 (10329 voxels, overlap=0.363)\n", "Brain_Stem (16): linear fit = 1.18 x + 0.0 (10329 voxels, peak = 92), gca=92.4\n", "gca peak = 0.12854 (88)\n", "mri peak = 0.08940 (101)\n", "Right_VentralDC (60): linear fit = 1.20 x + 0.0 (1512 voxels, overlap=0.017)\n", "Right_VentralDC (60): linear fit = 1.20 x + 0.0 (1512 voxels, peak = 105), gca=105.2\n", "gca peak = 0.15703 (87)\n", "mri peak = 0.10143 (101)\n", "Left_VentralDC (28): linear fit = 1.20 x + 0.0 (1493 voxels, overlap=0.012)\n", "Left_VentralDC (28): linear fit = 1.20 x + 0.0 (1493 voxels, peak = 104), gca=104.0\n", "gca peak = 0.17522 (25)\n", "mri peak = 0.42105 ( 9)\n", "gca peak = 0.17113 (14)\n", "mri peak = 0.35667 ( 3)\n", "Fourth_Ventricle (15): linear fit = 0.12 x + 0.0 (291 voxels, overlap=0.016)\n", "Fourth_Ventricle (15): linear fit = 0.12 x + 0.0 (291 voxels, peak = 2), gca=1.8\n", "gca peak Unknown = 0.94777 ( 0)\n", "gca peak Left_Inf_Lat_Vent = 0.16627 (28)\n", "gca peak Third_Ventricle = 0.17522 (25)\n", "gca peak Fourth_Ventricle = 0.17113 (14)\n", "gca peak CSF = 0.20346 (36)\n", "gca peak Left_Accumbens_area = 0.70646 (62)\n", "gca peak Left_undetermined = 1.00000 (28)\n", "gca peak Left_vessel = 0.89917 (53)\n", "gca peak Left_choroid_plexus = 0.11689 (35)\n", "gca peak Right_Inf_Lat_Vent = 0.25504 (23)\n", "gca peak Right_Accumbens_area = 0.31650 (65)\n", "gca peak Right_vessel = 0.77268 (52)\n", "gca peak Right_choroid_plexus = 0.13275 (38)\n", "gca peak Fifth_Ventricle = 0.60973 (33)\n", "gca peak WM_hypointensities = 0.11013 (77)\n", "gca peak non_WM_hypointensities = 0.11354 (41)\n", "gca peak Optic_Chiasm = 0.51646 (76)\n", "not using caudate to estimate GM means\n", "estimating mean gm scale to be 1.06 x + 0.0\n", "estimating mean wm scale to be 1.00 x + 0.0\n", "estimating mean csf scale to be 0.41 x + 0.0\n", "Left_Pallidum too bright - rescaling by 0.924 (from 1.125) to 100.9 (was 109.1)\n", "Right_Pallidum too bright - rescaling by 0.960 (from 1.095) to 100.9 (was 105.1)\n", "saving intensity scales to aseg.auto_noCCseg.label_intensities.txt\n", "renormalizing by structure alignment....\n", "renormalizing input #0\n", "gca peak = 0.31706 ( 7)\n", "mri peak = 0.17945 ( 7)\n", "Left_Lateral_Ventricle (4): linear fit = 0.82 x + 0.0 (1560 voxels, overlap=0.926)\n", "Left_Lateral_Ventricle (4): linear fit = 0.82 x + 0.0 (1560 voxels, peak = 6), gca=5.8\n", "gca peak = 0.29738 ( 6)\n", "mri peak = 0.17272 ( 7)\n", "Right_Lateral_Ventricle (43): linear fit = 1.25 x + 0.0 (1589 voxels, overlap=0.924)\n", "Right_Lateral_Ventricle (43): linear fit = 1.25 x + 0.0 (1589 voxels, peak = 7), gca=7.5\n", "gca peak = 0.28156 (100)\n", "mri peak = 0.16332 (106)\n", "Right_Pallidum (52): linear fit = 1.04 x + 0.0 (819 voxels, overlap=0.821)\n", "Right_Pallidum (52): linear fit = 1.04 x + 0.0 (819 voxels, peak = 104), gca=104.5\n", "gca peak = 0.15478 (99)\n", "mri peak = 0.11072 (106)\n", "Left_Pallidum (13): linear fit = 1.08 x + 0.0 (858 voxels, overlap=0.466)\n", "Left_Pallidum (13): linear fit = 1.08 x + 0.0 (858 voxels, peak = 106), gca=106.4\n", "gca peak = 0.26416 (56)\n", "mri peak = 0.10696 (56)\n", "Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (782 voxels, overlap=1.011)\n", "Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (782 voxels, peak = 56), gca=56.0\n", "gca peak = 0.33569 (58)\n", "mri peak = 0.09347 (60)\n", "Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (838 voxels, overlap=1.009)\n", "Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (838 voxels, peak = 57), gca=57.1\n", "gca peak = 0.07621 (103)\n", "mri peak = 0.13857 (102)\n", "Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (41973 voxels, overlap=0.615)\n", "Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (41973 voxels, peak = 103), gca=103.0\n", "gca peak = 0.07845 (105)\n", "mri peak = 0.13751 (104)\n", "Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (43265 voxels, overlap=0.620)\n", "Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (43265 voxels, peak = 105), gca=105.0\n", "gca peak = 0.08782 (63)\n", "mri peak = 0.04398 (66)\n", "Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (29448 voxels, overlap=0.960)\n", "Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (29448 voxels, peak = 63), gca=63.0\n", "gca peak = 0.10681 (63)\n", "mri peak = 0.04406 (64)\n", "Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (28388 voxels, overlap=0.926)\n", "Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (28388 voxels, peak = 65), gca=64.6\n", "gca peak = 0.22478 (74)\n", "mri peak = 0.18231 (76)\n", "Right_Caudate (50): linear fit = 1.00 x + 0.0 (935 voxels, overlap=1.000)\n", "Right_Caudate (50): linear fit = 1.00 x + 0.0 (935 voxels, peak = 74), gca=74.0\n", "gca peak = 0.14473 (69)\n", "mri peak = 0.13884 (77)\n", "Left_Caudate (11): linear fit = 1.00 x + 0.0 (901 voxels, overlap=0.937)\n", "Left_Caudate (11): linear fit = 1.00 x + 0.0 (901 voxels, peak = 69), gca=69.0\n", "gca peak = 0.16470 (48)\n", "mri peak = 0.05310 (48)\n", "Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (14929 voxels, overlap=1.000)\n", "Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (14929 voxels, peak = 48), gca=48.0\n", "gca peak = 0.18229 (46)\n", "mri peak = 0.04965 (46)\n", "Right_Cerebellum_Cortex (47): linear fit = 1.05 x + 0.0 (15407 voxels, overlap=0.996)\n", "Right_Cerebellum_Cortex (47): linear fit = 1.05 x + 0.0 (15407 voxels, peak = 49), gca=48.5\n", "gca peak = 0.15119 (90)\n", "mri peak = 0.07994 (89)\n", "Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5075 voxels, overlap=0.982)\n", "Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5075 voxels, peak = 90), gca=89.6\n", "gca peak = 0.16700 (90)\n", "mri peak = 0.08530 (88)\n", "Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (5192 voxels, overlap=0.982)\n", "Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (5192 voxels, peak = 89), gca=88.7\n", "gca peak = 0.23301 (63)\n", "mri peak = 0.10000 (63)\n", "Left_Amygdala (18): linear fit = 1.01 x + 0.0 (469 voxels, overlap=1.028)\n", "Left_Amygdala (18): linear fit = 1.01 x + 0.0 (469 voxels, peak = 64), gca=63.9\n", "gca peak = 0.29567 (63)\n", "mri peak = 0.11073 (62)\n", "Right_Amygdala (54): linear fit = 1.00 x + 0.0 (449 voxels, overlap=1.021)\n", "Right_Amygdala (54): linear fit = 1.00 x + 0.0 (449 voxels, peak = 63), gca=63.0\n", "gca peak = 0.10834 (95)\n", "mri peak = 0.08778 (91)\n", "Left_Thalamus (10): linear fit = 0.99 x + 0.0 (4105 voxels, overlap=0.971)\n", "Left_Thalamus (10): linear fit = 0.99 x + 0.0 (4105 voxels, peak = 94), gca=93.6\n", "gca peak = 0.11610 (91)\n", "mri peak = 0.08291 (89)\n", "Right_Thalamus (49): linear fit = 1.00 x + 0.0 (4093 voxels, overlap=0.955)\n", "Right_Thalamus (49): linear fit = 1.00 x + 0.0 (4093 voxels, peak = 91), gca=91.0\n", "gca peak = 0.07778 (89)\n", "mri peak = 0.09072 (84)\n", "Left_Putamen (12): linear fit = 1.00 x + 0.0 (1968 voxels, overlap=0.718)\n", "Left_Putamen (12): linear fit = 1.00 x + 0.0 (1968 voxels, peak = 89), gca=89.0\n", "gca peak = 0.08743 (83)\n", "mri peak = 0.09372 (88)\n", "Right_Putamen (51): linear fit = 1.00 x + 0.0 (2102 voxels, overlap=0.840)\n", "Right_Putamen (51): linear fit = 1.00 x + 0.0 (2102 voxels, peak = 83), gca=83.0\n", "gca peak = 0.07618 (93)\n", "mri peak = 0.06509 (96)\n", "Brain_Stem (16): linear fit = 0.98 x + 0.0 (10329 voxels, overlap=0.855)\n", "Brain_Stem (16): linear fit = 0.98 x + 0.0 (10329 voxels, peak = 91), gca=90.7\n", "gca peak = 0.10886 (105)\n", "mri peak = 0.08940 (101)\n", "Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1512 voxels, overlap=0.835)\n", "Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1512 voxels, peak = 106), gca=105.5\n", "gca peak = 0.16520 (102)\n", "mri peak = 0.10143 (101)\n", "Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1493 voxels, overlap=0.880)\n", "Left_VentralDC (28): linear fit = 0.99 x + 0.0 (1493 voxels, peak = 100), gca=100.5\n", "gca peak = 0.33670 (11)\n", "mri peak = 0.42105 ( 9)\n", "gca peak = 0.38155 ( 6)\n", "mri peak = 0.35667 ( 3)\n", "Fourth_Ventricle (15): linear fit = 0.32 x + 0.0 (291 voxels, overlap=0.435)\n", "Fourth_Ventricle (15): linear fit = 0.32 x + 0.0 (291 voxels, peak = 2), gca=1.9\n", "gca peak Unknown = 0.94777 ( 0)\n", "gca peak Left_Inf_Lat_Vent = 0.20560 (29)\n", "gca peak Third_Ventricle = 0.33670 (11)\n", "gca peak Fourth_Ventricle = 0.38155 ( 6)\n", "gca peak CSF = 0.34330 (15)\n", "gca peak Left_Accumbens_area = 0.61521 (62)\n", "gca peak Left_undetermined = 1.00000 (28)\n", "gca peak Left_vessel = 0.89917 (53)\n", "gca peak Left_choroid_plexus = 0.11689 (35)\n", "gca peak Right_Inf_Lat_Vent = 0.25695 (23)\n", "gca peak Right_Accumbens_area = 0.37254 (72)\n", "gca peak Right_vessel = 0.77268 (52)\n", "gca peak Right_choroid_plexus = 0.13275 (38)\n", "gca peak Fifth_Ventricle = 0.59846 (14)\n", "gca peak WM_hypointensities = 0.11042 (77)\n", "gca peak non_WM_hypointensities = 0.11354 (41)\n", "gca peak Optic_Chiasm = 0.54524 (76)\n", "not using caudate to estimate GM means\n", "estimating mean gm scale to be 1.00 x + 0.0\n", "estimating mean wm scale to be 1.00 x + 0.0\n", "estimating mean csf scale to be 1.03 x + 0.0\n", "Left_Pallidum too bright - rescaling by 0.948 (from 1.075) to 100.9 (was 106.4)\n", "Right_Pallidum too bright - rescaling by 0.965 (from 1.045) to 100.9 (was 104.5)\n", "saving intensity scales to aseg.auto_noCCseg.label_intensities.txt\n", "saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt\n" ] } ], "source": [ "!mkdir ./freesurfer_output\n", "!recon-all -subject subjectname -i mp2rage.nii -all -sd ./freesurfer_output" ] }, { "cell_type": "code", "execution_count": 3, "id": "0c23ecb0-86ff-4428-b6e3-d1754d586f1d", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "T1.mgz\t\t\t\t\t mri_nu_correct.mni.log.bak\n", "antsdn.brain.mgz\t\t\t norm.mgz\n", "aparc+aseg.mgz\t\t\t\t nu.mgz\n", "aparc.DKTatlas+aseg.mgz\t\t\t orig\n", "aparc.a2009s+aseg.mgz\t\t\t orig.mgz\n", "aseg.auto.mgz\t\t\t\t orig_nu.mgz\n", "aseg.auto_noCCseg.label_intensities.txt rawavg.mgz\n", "aseg.auto_noCCseg.mgz\t\t\t rh.ribbon.mgz\n", "aseg.mgz\t\t\t\t ribbon.mgz\n", "aseg.presurf.hypos.mgz\t\t\t segment.dat\n", "aseg.presurf.mgz\t\t\t surface.defects.mgz\n", "brain.finalsurfs.mgz\t\t\t talairach.label_intensities.txt\n", "brain.mgz\t\t\t\t talairach.log\n", "brainmask.auto.mgz\t\t\t talairach_with_skull.log\n", "brainmask.mgz\t\t\t\t transforms\n", "ctrl_pts.mgz\t\t\t\t wm.asegedit.mgz\n", "filled.auto.mgz\t\t\t\t wm.mgz\n", "filled.mgz\t\t\t\t wm.seg.mgz\n", "lh.ribbon.mgz\t\t\t\t wmparc.mgz\n", "mri_nu_correct.mni.log\n" ] } ], "source": [ "!ls ./freesurfer_output/subjectname/mri" ] }, { "cell_type": "code", "execution_count": 6, "id": "ee2bb1f2-043a-4221-bc80-0a773740d134", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "autodet.gw.stats.lh.dat lh.smoothwm.K1.crv\t rh.inflated.nofix\n", "autodet.gw.stats.rh.dat lh.smoothwm.K2.crv\t rh.jacobian_white\n", "lh.area\t\t\t lh.smoothwm.S.crv\t rh.orig\n", "lh.area.mid\t\t lh.smoothwm.nofix\t rh.orig.nofix\n", "lh.area.pial\t\t lh.sphere\t\t rh.orig.premesh\n", "lh.avg_curv\t\t lh.sphere.reg\t\t rh.pial\n", "lh.curv\t\t\t lh.sulc\t\t rh.pial.T1\n", "lh.curv.pial\t\t lh.thickness\t\t rh.qsphere.nofix\n", "lh.defect_borders\t lh.volume\t\t rh.smoothwm\n", "lh.defect_chull\t\t lh.w-g.pct.mgh\t\t rh.smoothwm.BE.crv\n", "lh.defect_labels\t lh.white\t\t rh.smoothwm.C.crv\n", "lh.defects.pointset\t lh.white.H\t\t rh.smoothwm.FI.crv\n", "lh.fsaverage.sphere.reg lh.white.K\t\t rh.smoothwm.H.crv\n", "lh.inflated\t\t lh.white.preaparc\t rh.smoothwm.K.crv\n", "lh.inflated.H\t\t lh.white.preaparc.H\t rh.smoothwm.K1.crv\n", "lh.inflated.K\t\t lh.white.preaparc.K\t rh.smoothwm.K2.crv\n", "lh.inflated.nofix\t rh.area\t\t rh.smoothwm.S.crv\n", "lh.jacobian_white\t rh.area.mid\t\t rh.smoothwm.nofix\n", "lh.orig\t\t\t rh.area.pial\t\t rh.sphere\n", "lh.orig.nofix\t\t rh.avg_curv\t\t rh.sphere.reg\n", "lh.orig.premesh\t\t rh.curv\t\t rh.sulc\n", "lh.pial\t\t\t rh.curv.pial\t\t rh.thickness\n", "lh.pial.T1\t\t rh.defect_borders\t rh.volume\n", "lh.qsphere.nofix\t rh.defect_chull\t rh.w-g.pct.mgh\n", "lh.smoothwm\t\t rh.defect_labels\t rh.white\n", "lh.smoothwm.BE.crv\t rh.defects.pointset\t rh.white.H\n", "lh.smoothwm.C.crv\t rh.fsaverage.sphere.reg rh.white.K\n", "lh.smoothwm.FI.crv\t rh.inflated\t\t rh.white.preaparc\n", "lh.smoothwm.H.crv\t rh.inflated.H\t\t rh.white.preaparc.H\n", "lh.smoothwm.K.crv\t rh.inflated.K\t\t rh.white.preaparc.K\n" ] } ], "source": [ "!ls ./freesurfer_output/subjectname/surf" ] }, { "cell_type": "code", "execution_count": 7, "id": "ea0da756-e384-4a79-88e6-9023b574593e", "metadata": { "tags": [] }, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "a61b9294a6d446f4802d9d0f705f333c", "version_major": 2, "version_minor": 0 }, "text/plain": [ "ipyniivue.Niivue(back_color=[0.0, 0.0, 0.0, 1.0], clip_plane_color=[1.0, 1.0, 1.0, 0.5], crosshair_color=[0.0,…" ] }, "execution_count": 7, "metadata": {}, "output_type": "execute_result" } ], "source": [ "import ipyniivue\n", "nv = ipyniivue.Niivue(crosshair_color=[0,1,0,1])\n", "nv.add_volume('./freesurfer_output/subjectname/mri/orig.mgz')\n", "nv.add_volume('./freesurfer_output/subjectname/mri/aseg.mgz')" ] } ], "metadata": { "colab": { "include_colab_link": true, "provenance": [] }, "kernelspec": { "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.10.4" } }, "nbformat": 4, "nbformat_minor": 5 }