{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "\"Open " ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "# Brain extraction with different software packages\n", "\n", "Author: Monika Doerig\n", "\n", "### Citation:\n", "__Andy's Brain Book:__\n", "\n", "- This brain extraction example is based on the [Advanced Normalization Tools (ANTs)](https://andysbrainbook.readthedocs.io/en/latest/ANTs/ANTs_Overview.html) chapter from Andy’s Brain Book (Jahn, 2022. [doi:10.5281/zenodo.5879293](https://zenodo.org/records/5879294))\n", "\n", "__SynthStrip:__\n", "\n", "- SynthStrip: Skull-Stripping for Any Brain Image; Andrew Hoopes, Jocelyn S. Mora, Adrian V. Dalca, Bruce Fischl*, Malte Hoffmann* (*equal contribution); NeuroImage 260, 2022, 119474; https://doi.org/10.1016/j.neuroimage.2022.119474\n", "- Boosting skull-stripping performance for pediatric brain images; William Kelley, Nathan Ngo, Adrian V. Dalca, Bruce Fischl, Lilla Zöllei*, Malte Hoffmann* (*equal contribution); IEEE International Symposium on Biomedical Imaging (ISBI), 2024, forthcoming; https://arxiv.org/abs/2402.16634\n", "- SynthStrip tool: https://w3id.org/synthstrip\n", "\n", "__Opensource Data from OpenNeuro:__\n", "- Kelly AMC and Uddin LQ and Biswal BB and Castellanos FX and Milham MP (2018). Flanker task (event-related). [OpenNeuro Dataset ds000102](https://openneuro.org/datasets/ds000102/versions/00001)\n", "- Kelly, A.M., Uddin, L.Q., Biswal, B.B., Castellanos, F.X., Milham, M.P. (2008). Competition between functional brain networks mediates behavioral variability. Neuroimage, 39(1):527-37\n", "\n", "__ANTs Brain Templates:__\n", "- Avants, Brian; Tustison, Nick (2018). ANTs/ANTsR Brain Templates. figshare. Dataset. https://doi.org/10.6084/m9.figshare.915436.v2\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Setup Neurodesk" ] }, { "cell_type": "code", "execution_count": 1, "metadata": { "vscode": { "languageId": "plaintext" } }, "outputs": [], "source": [ "%%capture\n", "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/')))))" ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "tags": [] }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "vendor_id\t: GenuineIntel\n", "model name\t: Intel(R) Xeon(R) Gold 6126 CPU @ 2.60GHz\n" ] } ], "source": [ "# Output CPU information:\n", "!cat /proc/cpuinfo | grep 'vendor' | uniq\n", "!cat /proc/cpuinfo | grep 'model name' | uniq" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Introduction\n", "Since fMRI studies focus on brain tissue, our first step is to remove the skull and non-brain areas from the image.\n", "\n", "In order to analyze fMRI data, you will need to load an fMRI analysis package. In this example we will use the following packages and algorithms to skull-strip the anatomical image:\n", "\n", " Advanced Normalization Tools (ANTs): antsBrainExtraction.sh\n", "\n", " Analysis of Functional NeuroImages (AFNI): 3dSkullStrip\n", "\n", " FreeSurfer: SynthStrip\n", "\n", " FSL (FMRIB Software Library, created by the University of Oxford): BET - Brain Extraction Tool\n", "\n", "\n", "Each package is maintained by a team of professionals, and each is updated at least every few years or so." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Advanced Normalization Tools (ANTs)\n", "ANTs is a software package for normalizing data to a template.\n", "\n", "Templates for public neuroimaging datasets, such as those from IXI, Oasis, NKI-1, and Kirby/MMRR, are intended for use with ANTs and are available for download from [figshare](https://doi.org/10.6084/m9.figshare.915436.v2). These templates include an average T1 neuroimage of the head and various tissue priors for cortex, white matter, cerebrospinal fluid, deep gray matter, brainstem and the cerebellum." ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "['ants/2.3.1']" ] }, "execution_count": 3, "metadata": {}, "output_type": "execute_result" } ], "source": [ "import lmod\n", "await lmod.load('ants/2.3.1')\n", "await lmod.list()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### Analysis of Functional NeuroImages (AFNI)\n", "AFNI is a suite of programs designed to analyze fMRI data. Created in the mid-1990’s by Bob Cox, AFNI is now used by hundreds of imaging labs around the world." ] }, { "cell_type": "code", "execution_count": 4, "metadata": { "vscode": { "languageId": "plaintext" } }, "outputs": [ { "data": { "text/plain": [ "['ants/2.3.1', 'afni/24.1.02']" ] }, "execution_count": 4, "metadata": {}, "output_type": "execute_result" } ], "source": [ "await lmod.load('afni/24.1.02')\n", "await lmod.list()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### FreeSurfer\n", "FreeSurfer is a software package that enables you to analyze structural MRI images - in other words, you can use FreeSurfer to quantify the amount of grey matter and white matter in specific regions of the brain. You will also be able to calculate measurements such as the thickness, curvature, and volume of the different tissue types, and be able to correlate these with covariates; or, you can contrast these structural measurements between groups." ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "['ants/2.3.1', 'afni/24.1.02', 'freesurfer/7.3.2']" ] }, "execution_count": 5, "metadata": {}, "output_type": "execute_result" } ], "source": [ "await lmod.load('freesurfer/7.3.2')\n", "await lmod.list()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### FMRIB Software Library (FSL)\n", "FSL is a comprehensive library of analysis tools for FMRI, MRI and diffusion brain imaging data. \n", "FSL has a tool to skull-strip an anatomical image called bet, or the Brain Extraction Tool." ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "['ants/2.3.1', 'afni/24.1.02', 'freesurfer/7.3.2', 'fsl/6.0.7.4']" ] }, "execution_count": 6, "metadata": {}, "output_type": "execute_result" } ], "source": [ "await lmod.load('fsl/6.0.7.4')\n", "await lmod.list()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Download Data\n", "\n", "### T1 Image for brain extraction" ] }, { "cell_type": "code", "execution_count": 7, "metadata": { "scrolled": true, "vscode": { "languageId": "plaintext" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Total: 0%| | 0.00/10.6M [00:00] 52.80M 43.6MB/s in 1.2s \n", "\n", "2024-11-04 08:17:11 (43.6 MB/s) - ‘OASIS.zip’ saved [55360609/55360609]\n", "\n", "Archive: OASIS.zip\n", " inflating: OASIS/MICCAI2012-Multi-Atlas-Challenge-Data/T_template0.nii.gz \n", " inflating: OASIS/MICCAI2012-Multi-Atlas-Challenge-Data/T_template0_BrainCerebellum.nii.gz \n", " inflating: OASIS/MICCAI2012-Multi-Atlas-Challenge-Data/T_template0_BrainCerebellumExtractionMask.nii.gz \n", " inflating: OASIS/MICCAI2012-Multi-Atlas-Challenge-Data/T_template0_BrainCerebellumMask.nii.gz \n", " inflating: OASIS/MICCAI2012-Multi-Atlas-Challenge-Data/T_template0_BrainCerebellumProbabilityMask.nii.gz \n", " inflating: OASIS/MICCAI2012-Multi-Atlas-Challenge-Data/T_template0_BrainCerebellumRegistrationMask.nii.gz \n", " inflating: OASIS/MICCAI2012-Multi-Atlas-Challenge-Data/T_template0_glm_4labelsJointFusion.nii.gz \n", " inflating: OASIS/MICCAI2012-Multi-Atlas-Challenge-Data/T_template0_glm_6labelsJointFusion.nii.gz \n", " creating: OASIS/MICCAI2012-Multi-Atlas-Challenge-Data/Priors2/\n", " inflating: OASIS/MICCAI2012-Multi-Atlas-Challenge-Data/Priors2/priors1.nii.gz \n", " inflating: OASIS/MICCAI2012-Multi-Atlas-Challenge-Data/Priors2/priors2.nii.gz \n", " inflating: OASIS/MICCAI2012-Multi-Atlas-Challenge-Data/Priors2/priors3.nii.gz \n", " inflating: OASIS/MICCAI2012-Multi-Atlas-Challenge-Data/Priors2/priors4.nii.gz \n", " inflating: OASIS/MICCAI2012-Multi-Atlas-Challenge-Data/Priors2/priors5.nii.gz \n", " inflating: OASIS/MICCAI2012-Multi-Atlas-Challenge-Data/Priors2/priors6.nii.gz \n" ] } ], "source": [ "# Download the OASIS templates using wget\n", "! wget https://ndownloader.figshare.com/files/3133832 -O OASIS.zip\n", "\n", "# Unzip the downloaded file\n", "! unzip OASIS.zip -d OASIS\n", "\n", "# Remove zip file\n", "! rm OASIS.zip\n", "\n", "# Delete templates that are not needed\n", "! find OASIS/MICCAI2012-Multi-Atlas-Challenge-Data -type f ! -name 'T_template0.nii.gz' ! -name 'T_template0_BrainCerebellumProbabilityMask.nii.gz' -exec rm {} +\n", "\n", "# Delete Priors2 subfolder\n", "! rm -r OASIS/MICCAI2012-Multi-Atlas-Challenge-Data/Priors2" ] }, { "cell_type": "code", "execution_count": 10, "metadata": {}, "outputs": [], "source": [ "brain_template = 'OASIS/MICCAI2012-Multi-Atlas-Challenge-Data/T_template0.nii.gz'\n", "brain_prior = 'OASIS/MICCAI2012-Multi-Atlas-Challenge-Data/T_template0_BrainCerebellumProbabilityMask.nii.gz'" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Brain Extraction" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### 1. ANTs\n", "First, we will perform brain extraction with this ANTs commands:" ] }, { "cell_type": "code", "execution_count": 11, "metadata": { "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n", "antsBrainExtraction.sh performs template-based brain extraction.\n", "\n", "Usage:\n", "\n", "antsBrainExtraction.sh -d imageDimension\n", " -a anatomicalImage\n", " -e brainExtractionTemplate\n", " -m brainExtractionProbabilityMask\n", " \n", " -o outputPrefix\n", "\n", "Example:\n", "\n", " bash /opt/ants-2.3.1/antsBrainExtraction.sh -d 3 -a t1.nii.gz -e brainWithSkullTemplate.nii.gz -m brainPrior.nii.gz -o output\n", "\n", "Required arguments:\n", "\n", " -d: Image dimension 2 or 3 (for 2- or 3-dimensional image)\n", " -a: Anatomical image Structural image, typically T1. If more than one\n", " anatomical image is specified, subsequently specified\n", " images are used during the segmentation process. However,\n", " only the first image is used in the registration of priors.\n", " Our suggestion would be to specify the T1 as the first image.\n", " -e: Brain extraction template Anatomical template created using e.g. LPBA40 data set with\n", " buildtemplateparallel.sh in ANTs.\n", " -m: Brain extraction probability mask Brain probability mask created using e.g. LPBA40 data set which\n", " have brain masks defined, and warped to anatomical template and\n", " averaged resulting in a probability image.\n", " -o: Output prefix Output directory + file prefix\n", "\n", "Optional arguments:\n", "\n", " -c: Tissue classification A k-means segmentation is run to find gray or white matter around \n", " the edge of the initial brain mask warped from the template.\n", " This produces a segmentation image with K classes, ordered by mean\n", " intensity in increasing order. With this option, you can control\n", " K and tell the script which classes represent CSF, gray and white matter. \n", " Format (\\\"KxcsfLabelxgmLabelxwmLabel\\\")\n", " Examples: \n", " -c 3x1x2x3 for T1 with K=3, CSF=1, GM=2, WM=3 (default)\n", " -c 3x3x2x1 for T2 with K=3, CSF=3, GM=2, WM=1\n", " -c 3x1x3x2 for FLAIR with K=3, CSF=1 GM=3, WM=2\n", " -c 4x4x2x3 uses K=4, CSF=4, GM=2, WM=3\n", "\n", " -f: Brain extraction registration mask Mask used for registration to limit the metric computation to\n", " a specific region.\n", " -s: image file suffix Any of the standard ITK IO formats e.g. nrrd, nii.gz (default), mhd\n", " -u: use random seeding Use random number generated from system clock in Atropos (default = 1)\n", " -k: keep temporary files Keep brain extraction/segmentation warps, etc (default = false).\n", " -q: use floating point precision Use antsRegistration with floating point precision.\n", "\n", " -z: Test / debug mode If > 0, runs a faster version of the script. Only for debugging, results will not be good.\n", "\n" ] } ], "source": [ "! antsBrainExtraction.sh" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "To run the command using the OASIS templates, you can follow this structure:" ] }, { "cell_type": "code", "execution_count": 12, "metadata": { "scrolled": true, "vscode": { "languageId": "plaintext" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " \n", "Will run Atropos segmentation with K=3. Classes labeled in order of mean intensity. Assuming CSF=1, GM=2, WM=3\n", "\n", "The output directory \"ANTS_Stripped_\" does not exist. Making it.\n", "\n", " Using antsBrainExtraction with the following arguments:\n", " image dimension = 3\n", " anatomical image = ds000102/sub-08/anat/sub-08_T1w.nii.gz\n", " extraction template = OASIS/MICCAI2012-Multi-Atlas-Challenge-Data/T_template0.nii.gz\n", " extraction reg. mask = \n", " extraction prior = OASIS/MICCAI2012-Multi-Atlas-Challenge-Data/T_template0_BrainCerebellumProbabilityMask.nii.gz\n", " output prefix = ANTS_Stripped_\n", " output image suffix = nii.gz\n", "\n", " N4 parameters (pre brain extraction):\n", " convergence = [50x50x50x50,0.0000001]\n", " shrink factor = 4\n", " B-spline parameters = [200]\n", "\n", " Atropos parameters (extraction):\n", " convergence = [3,0.0]\n", " likelihood = Gaussian\n", " initialization = kmeans[3]\n", " mrf = [0.1,1x1x1]\n", " use clock random seed = 1\n", "\n", "--------------------- Running antsBrainExtraction.sh on jupyter-monidoerig ---------------------\n", "\n", "--------------------------------------------------------------------------------------\n", " Bias correction of anatomical images (pre brain extraction)\n", " 1) pre-process by truncating the image intensities\n", " 2) run N4\n", "--------------------------------------------------------------------------------------\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "/opt/ants-2.3.1//ImageMath 3 ANTS_Stripped_N4Truncated0.nii.gz TruncateImageIntensity ds000102/sub-08/anat/sub-08_T1w.nii.gz 0.01 0.999 256\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "/opt/ants-2.3.1//N4BiasFieldCorrection -d 3 -i ANTS_Stripped_N4Truncated0.nii.gz -s 4 -c [50x50x50x50,0.0000001] -b [200] -o ANTS_Stripped_N4Corrected0.nii.gz --verbose 1\n", "\n", "Running N4 for 3-dimensional images.\n", "\n", "Mask not read. Using the entire image as the mask.\n", "\n", "Specified spline distance: 200mm\n", " original image size: [176, 256, 256]\n", " padded image size: [201, 401, 401]\n", " number of control points: [4, 5, 5]\n", "\n", "Current level = 1\n", " Iteration 1 (of 50). Current convergence value = 0.000258536 (threshold = 1e-07)\n", " Iteration 2 (of 50). Current convergence value = 0.000248828 (threshold = 1e-07)\n", " Iteration 3 (of 50). Current convergence value = 0.000240245 (threshold = 1e-07)\n", " Iteration 4 (of 50). Current convergence value = 0.000232668 (threshold = 1e-07)\n", " Iteration 5 (of 50). Current convergence value = 0.00022608 (threshold = 1e-07)\n", " Iteration 6 (of 50). Current convergence value = 0.000220297 (threshold = 1e-07)\n", " Iteration 7 (of 50). Current convergence value = 0.000214742 (threshold = 1e-07)\n", " Iteration 8 (of 50). Current convergence value = 0.000209961 (threshold = 1e-07)\n", " Iteration 9 (of 50). Current convergence value = 0.000205729 (threshold = 1e-07)\n", " Iteration 10 (of 50). Current convergence value = 0.000201525 (threshold = 1e-07)\n", " Iteration 11 (of 50). Current convergence value = 0.000197393 (threshold = 1e-07)\n", " Iteration 12 (of 50). Current convergence value = 0.000193677 (threshold = 1e-07)\n", " Iteration 13 (of 50). Current convergence value = 0.00019035 (threshold = 1e-07)\n", " Iteration 14 (of 50). Current convergence value = 0.000187294 (threshold = 1e-07)\n", " Iteration 15 (of 50). Current convergence value = 0.000184611 (threshold = 1e-07)\n", " Iteration 16 (of 50). Current convergence value = 0.000182274 (threshold = 1e-07)\n", " Iteration 17 (of 50). Current convergence value = 0.000180015 (threshold = 1e-07)\n", " Iteration 18 (of 50). Current convergence value = 0.000177968 (threshold = 1e-07)\n", " Iteration 19 (of 50). Current convergence value = 0.000176021 (threshold = 1e-07)\n", " Iteration 20 (of 50). Current convergence value = 0.000174094 (threshold = 1e-07)\n", " Iteration 21 (of 50). Current convergence value = 0.000171951 (threshold = 1e-07)\n", " Iteration 22 (of 50). Current convergence value = 0.000169746 (threshold = 1e-07)\n", " Iteration 23 (of 50). Current convergence value = 0.000167645 (threshold = 1e-07)\n", " Iteration 24 (of 50). Current convergence value = 0.000165552 (threshold = 1e-07)\n", " Iteration 25 (of 50). Current convergence value = 0.000163502 (threshold = 1e-07)\n", " Iteration 26 (of 50). Current convergence value = 0.000162474 (threshold = 1e-07)\n", " Iteration 27 (of 50). Current convergence value = 0.00016215 (threshold = 1e-07)\n", " Iteration 28 (of 50). Current convergence value = 0.000161625 (threshold = 1e-07)\n", " Iteration 29 (of 50). Current convergence value = 0.000160964 (threshold = 1e-07)\n", " Iteration 30 (of 50). Current convergence value = 0.000160438 (threshold = 1e-07)\n", " Iteration 31 (of 50). Current convergence value = 0.000159709 (threshold = 1e-07)\n", " Iteration 32 (of 50). Current convergence value = 0.000159056 (threshold = 1e-07)\n", " Iteration 33 (of 50). Current convergence value = 0.000158104 (threshold = 1e-07)\n", " Iteration 34 (of 50). Current convergence value = 0.000157114 (threshold = 1e-07)\n", " Iteration 35 (of 50). Current convergence value = 0.000155974 (threshold = 1e-07)\n", " Iteration 36 (of 50). Current convergence value = 0.000154861 (threshold = 1e-07)\n", " Iteration 37 (of 50). Current convergence value = 0.000153546 (threshold = 1e-07)\n", " Iteration 38 (of 50). Current convergence value = 0.000152239 (threshold = 1e-07)\n", " Iteration 39 (of 50). Current convergence value = 0.000151147 (threshold = 1e-07)\n", " Iteration 40 (of 50). Current convergence value = 0.000149921 (threshold = 1e-07)\n", " Iteration 41 (of 50). Current convergence value = 0.000148829 (threshold = 1e-07)\n", " Iteration 42 (of 50). Current convergence value = 0.000147763 (threshold = 1e-07)\n", " Iteration 43 (of 50). Current convergence value = 0.000146349 (threshold = 1e-07)\n", " Iteration 44 (of 50). Current convergence value = 0.00014523 (threshold = 1e-07)\n", " Iteration 45 (of 50). Current convergence value = 0.000144099 (threshold = 1e-07)\n", " Iteration 46 (of 50). Current convergence value = 0.000142761 (threshold = 1e-07)\n", " Iteration 47 (of 50). Current convergence value = 0.000141342 (threshold = 1e-07)\n", " Iteration 48 (of 50). Current convergence value = 0.000140069 (threshold = 1e-07)\n", " Iteration 49 (of 50). Current convergence value = 0.000138855 (threshold = 1e-07)\n", " Iteration 50 (of 50). Current convergence value = 0.000137506 (threshold = 1e-07)\n", "Current level = 2\n", " Iteration 1 (of 50). Current convergence value = 0.000342861 (threshold = 1e-07)\n", " Iteration 2 (of 50). Current convergence value = 0.000341625 (threshold = 1e-07)\n", " Iteration 3 (of 50). Current convergence value = 0.000340768 (threshold = 1e-07)\n", " Iteration 4 (of 50). Current convergence value = 0.000340175 (threshold = 1e-07)\n", " Iteration 5 (of 50). Current convergence value = 0.00033827 (threshold = 1e-07)\n", " Iteration 6 (of 50). Current convergence value = 0.000336399 (threshold = 1e-07)\n", " Iteration 7 (of 50). Current convergence value = 0.000334478 (threshold = 1e-07)\n", " Iteration 8 (of 50). Current convergence value = 0.000331891 (threshold = 1e-07)\n", " Iteration 9 (of 50). Current convergence value = 0.000329826 (threshold = 1e-07)\n", " Iteration 10 (of 50). Current convergence value = 0.000327873 (threshold = 1e-07)\n", " Iteration 11 (of 50). Current convergence value = 0.000326366 (threshold = 1e-07)\n", " Iteration 12 (of 50). Current convergence value = 0.000325203 (threshold = 1e-07)\n", " Iteration 13 (of 50). Current convergence value = 0.000324245 (threshold = 1e-07)\n", " Iteration 14 (of 50). Current convergence value = 0.000323119 (threshold = 1e-07)\n", " Iteration 15 (of 50). Current convergence value = 0.000322634 (threshold = 1e-07)\n", " Iteration 16 (of 50). Current convergence value = 0.000322995 (threshold = 1e-07)\n", " Iteration 17 (of 50). Current convergence value = 0.00032329 (threshold = 1e-07)\n", " Iteration 18 (of 50). Current convergence value = 0.000323898 (threshold = 1e-07)\n", " Iteration 19 (of 50). Current convergence value = 0.000324528 (threshold = 1e-07)\n", " Iteration 20 (of 50). Current convergence value = 0.000321647 (threshold = 1e-07)\n", " Iteration 21 (of 50). Current convergence value = 0.000318242 (threshold = 1e-07)\n", " Iteration 22 (of 50). Current convergence value = 0.000315148 (threshold = 1e-07)\n", " Iteration 23 (of 50). Current convergence value = 0.000312036 (threshold = 1e-07)\n", " Iteration 24 (of 50). Current convergence value = 0.000309086 (threshold = 1e-07)\n", " Iteration 25 (of 50). Current convergence value = 0.00030673 (threshold = 1e-07)\n", " Iteration 26 (of 50). Current convergence value = 0.00030398 (threshold = 1e-07)\n", " Iteration 27 (of 50). Current convergence value = 0.000301205 (threshold = 1e-07)\n", " Iteration 28 (of 50). Current convergence value = 0.000298513 (threshold = 1e-07)\n", " Iteration 29 (of 50). Current convergence value = 0.000295251 (threshold = 1e-07)\n", " Iteration 30 (of 50). Current convergence value = 0.000288666 (threshold = 1e-07)\n", " Iteration 31 (of 50). Current convergence value = 0.000270682 (threshold = 1e-07)\n", " Iteration 32 (of 50). Current convergence value = 0.000259328 (threshold = 1e-07)\n", " Iteration 33 (of 50). Current convergence value = 0.000247768 (threshold = 1e-07)\n", " Iteration 34 (of 50). Current convergence value = 0.00023528 (threshold = 1e-07)\n", " Iteration 35 (of 50). Current convergence value = 0.000224417 (threshold = 1e-07)\n", " Iteration 36 (of 50). Current convergence value = 0.000218353 (threshold = 1e-07)\n", " Iteration 37 (of 50). Current convergence value = 0.000213534 (threshold = 1e-07)\n", " Iteration 38 (of 50). Current convergence value = 0.000210124 (threshold = 1e-07)\n", " Iteration 39 (of 50). Current convergence value = 0.000207168 (threshold = 1e-07)\n", " Iteration 40 (of 50). Current convergence value = 0.000205513 (threshold = 1e-07)\n", " Iteration 41 (of 50). Current convergence value = 0.000205272 (threshold = 1e-07)\n", " Iteration 42 (of 50). Current convergence value = 0.000204942 (threshold = 1e-07)\n", " Iteration 43 (of 50). Current convergence value = 0.000204254 (threshold = 1e-07)\n", " Iteration 44 (of 50). Current convergence value = 0.000202326 (threshold = 1e-07)\n", " Iteration 45 (of 50). Current convergence value = 0.000199774 (threshold = 1e-07)\n", " Iteration 46 (of 50). Current convergence value = 0.000197384 (threshold = 1e-07)\n", " Iteration 47 (of 50). Current convergence value = 0.000195031 (threshold = 1e-07)\n", " Iteration 48 (of 50). Current convergence value = 0.000193075 (threshold = 1e-07)\n", " Iteration 49 (of 50). Current convergence value = 0.00019113 (threshold = 1e-07)\n", " Iteration 50 (of 50). Current convergence value = 0.0001893 (threshold = 1e-07)\n", "Current level = 3\n", " Iteration 1 (of 50). Current convergence value = 0.000998225 (threshold = 1e-07)\n", " Iteration 2 (of 50). Current convergence value = 0.000911791 (threshold = 1e-07)\n", " Iteration 3 (of 50). Current convergence value = 0.000837971 (threshold = 1e-07)\n", " Iteration 4 (of 50). Current convergence value = 0.000763517 (threshold = 1e-07)\n", " Iteration 5 (of 50). Current convergence value = 0.000704851 (threshold = 1e-07)\n", " Iteration 6 (of 50). Current convergence value = 0.00065979 (threshold = 1e-07)\n", " Iteration 7 (of 50). Current convergence value = 0.000624687 (threshold = 1e-07)\n", " Iteration 8 (of 50). Current convergence value = 0.000589346 (threshold = 1e-07)\n", " Iteration 9 (of 50). Current convergence value = 0.000554393 (threshold = 1e-07)\n", " Iteration 10 (of 50). Current convergence value = 0.000525235 (threshold = 1e-07)\n", " Iteration 11 (of 50). Current convergence value = 0.000501895 (threshold = 1e-07)\n", " Iteration 12 (of 50). Current convergence value = 0.000483087 (threshold = 1e-07)\n", " Iteration 13 (of 50). Current convergence value = 0.000468356 (threshold = 1e-07)\n", " Iteration 14 (of 50). Current convergence value = 0.000457002 (threshold = 1e-07)\n", " Iteration 15 (of 50). Current convergence value = 0.000448627 (threshold = 1e-07)\n", " Iteration 16 (of 50). Current convergence value = 0.000442205 (threshold = 1e-07)\n", " Iteration 17 (of 50). Current convergence value = 0.000437965 (threshold = 1e-07)\n", " Iteration 18 (of 50). Current convergence value = 0.000434013 (threshold = 1e-07)\n", " Iteration 19 (of 50). Current convergence value = 0.000430327 (threshold = 1e-07)\n", " Iteration 20 (of 50). Current convergence value = 0.000422352 (threshold = 1e-07)\n", " Iteration 21 (of 50). Current convergence value = 0.000408076 (threshold = 1e-07)\n", " Iteration 22 (of 50). Current convergence value = 0.000395871 (threshold = 1e-07)\n", " Iteration 23 (of 50). Current convergence value = 0.0003853 (threshold = 1e-07)\n", " Iteration 24 (of 50). Current convergence value = 0.000375409 (threshold = 1e-07)\n", " Iteration 25 (of 50). Current convergence value = 0.000366843 (threshold = 1e-07)\n", " Iteration 26 (of 50). Current convergence value = 0.000359712 (threshold = 1e-07)\n", " Iteration 27 (of 50). Current convergence value = 0.000353946 (threshold = 1e-07)\n", " Iteration 28 (of 50). Current convergence value = 0.000349232 (threshold = 1e-07)\n", " Iteration 29 (of 50). Current convergence value = 0.000345705 (threshold = 1e-07)\n", " Iteration 30 (of 50). Current convergence value = 0.000343062 (threshold = 1e-07)\n", " Iteration 31 (of 50). Current convergence value = 0.000341917 (threshold = 1e-07)\n", " Iteration 32 (of 50). Current convergence value = 0.000342084 (threshold = 1e-07)\n", " Iteration 33 (of 50). Current convergence value = 0.000343344 (threshold = 1e-07)\n", " Iteration 34 (of 50). Current convergence value = 0.00034619 (threshold = 1e-07)\n", " Iteration 35 (of 50). Current convergence value = 0.000350448 (threshold = 1e-07)\n", " Iteration 36 (of 50). Current convergence value = 0.000356079 (threshold = 1e-07)\n", " Iteration 37 (of 50). Current convergence value = 0.000363458 (threshold = 1e-07)\n", " Iteration 38 (of 50). Current convergence value = 0.000370693 (threshold = 1e-07)\n", " Iteration 39 (of 50). Current convergence value = 0.000363499 (threshold = 1e-07)\n", " Iteration 40 (of 50). Current convergence value = 0.000354278 (threshold = 1e-07)\n", " Iteration 41 (of 50). Current convergence value = 0.000344335 (threshold = 1e-07)\n", " Iteration 42 (of 50). Current convergence value = 0.000326012 (threshold = 1e-07)\n", " Iteration 43 (of 50). Current convergence value = 0.000283165 (threshold = 1e-07)\n", " Iteration 44 (of 50). Current convergence value = 0.000262942 (threshold = 1e-07)\n", " Iteration 45 (of 50). Current convergence value = 0.000256401 (threshold = 1e-07)\n", " Iteration 46 (of 50). Current convergence value = 0.000256516 (threshold = 1e-07)\n", " Iteration 47 (of 50). Current convergence value = 0.000259121 (threshold = 1e-07)\n", " Iteration 48 (of 50). Current convergence value = 0.000262287 (threshold = 1e-07)\n", " Iteration 49 (of 50). Current convergence value = 0.000265913 (threshold = 1e-07)\n", " Iteration 50 (of 50). Current convergence value = 0.000269532 (threshold = 1e-07)\n", "Current level = 4\n", " Iteration 1 (of 50). Current convergence value = 0.00146065 (threshold = 1e-07)\n", " Iteration 2 (of 50). Current convergence value = 0.0014295 (threshold = 1e-07)\n", " Iteration 3 (of 50). Current convergence value = 0.00134935 (threshold = 1e-07)\n", " Iteration 4 (of 50). Current convergence value = 0.00127588 (threshold = 1e-07)\n", " Iteration 5 (of 50). Current convergence value = 0.00122346 (threshold = 1e-07)\n", " Iteration 6 (of 50). Current convergence value = 0.00117814 (threshold = 1e-07)\n", " Iteration 7 (of 50). Current convergence value = 0.00114049 (threshold = 1e-07)\n", " Iteration 8 (of 50). Current convergence value = 0.00109704 (threshold = 1e-07)\n", " Iteration 9 (of 50). Current convergence value = 0.0010524 (threshold = 1e-07)\n", " Iteration 10 (of 50). Current convergence value = 0.00101912 (threshold = 1e-07)\n", " Iteration 11 (of 50). Current convergence value = 0.000998206 (threshold = 1e-07)\n", " Iteration 12 (of 50). Current convergence value = 0.000984174 (threshold = 1e-07)\n", " Iteration 13 (of 50). Current convergence value = 0.000974387 (threshold = 1e-07)\n", " Iteration 14 (of 50). Current convergence value = 0.000967613 (threshold = 1e-07)\n", " Iteration 15 (of 50). Current convergence value = 0.00096344 (threshold = 1e-07)\n", " Iteration 16 (of 50). Current convergence value = 0.000962287 (threshold = 1e-07)\n", " Iteration 17 (of 50). Current convergence value = 0.000964042 (threshold = 1e-07)\n", " Iteration 18 (of 50). Current convergence value = 0.000968691 (threshold = 1e-07)\n", " Iteration 19 (of 50). Current convergence value = 0.000974578 (threshold = 1e-07)\n", " Iteration 20 (of 50). Current convergence value = 0.000980622 (threshold = 1e-07)\n", " Iteration 21 (of 50). Current convergence value = 0.000988265 (threshold = 1e-07)\n", " Iteration 22 (of 50). Current convergence value = 0.000996283 (threshold = 1e-07)\n", " Iteration 23 (of 50). Current convergence value = 0.000980695 (threshold = 1e-07)\n", " Iteration 24 (of 50). Current convergence value = 0.000977463 (threshold = 1e-07)\n", " Iteration 25 (of 50). Current convergence value = 0.000974733 (threshold = 1e-07)\n", " Iteration 26 (of 50). Current convergence value = 0.000967454 (threshold = 1e-07)\n", " Iteration 27 (of 50). Current convergence value = 0.000956385 (threshold = 1e-07)\n", " Iteration 28 (of 50). Current convergence value = 0.00094419 (threshold = 1e-07)\n", " Iteration 29 (of 50). Current convergence value = 0.000928369 (threshold = 1e-07)\n", " Iteration 30 (of 50). Current convergence value = 0.000910889 (threshold = 1e-07)\n", " Iteration 31 (of 50). Current convergence value = 0.000896919 (threshold = 1e-07)\n", " Iteration 32 (of 50). Current convergence value = 0.000881585 (threshold = 1e-07)\n", " Iteration 33 (of 50). Current convergence value = 0.000863008 (threshold = 1e-07)\n", " Iteration 34 (of 50). Current convergence value = 0.000846915 (threshold = 1e-07)\n", " Iteration 35 (of 50). Current convergence value = 0.000831319 (threshold = 1e-07)\n", " Iteration 36 (of 50). Current convergence value = 0.00081534 (threshold = 1e-07)\n", " Iteration 37 (of 50). Current convergence value = 0.000798769 (threshold = 1e-07)\n", " Iteration 38 (of 50). Current convergence value = 0.000781479 (threshold = 1e-07)\n", " Iteration 39 (of 50). Current convergence value = 0.00076681 (threshold = 1e-07)\n", " Iteration 40 (of 50). Current convergence value = 0.000758623 (threshold = 1e-07)\n", " Iteration 41 (of 50). Current convergence value = 0.000749481 (threshold = 1e-07)\n", " Iteration 42 (of 50). Current convergence value = 0.000746784 (threshold = 1e-07)\n", " Iteration 43 (of 50). Current convergence value = 0.000746007 (threshold = 1e-07)\n", " Iteration 44 (of 50). Current convergence value = 0.000749525 (threshold = 1e-07)\n", " Iteration 45 (of 50). Current convergence value = 0.000754025 (threshold = 1e-07)\n", " Iteration 46 (of 50). Current convergence value = 0.000755228 (threshold = 1e-07)\n", " Iteration 47 (of 50). Current convergence value = 0.000758238 (threshold = 1e-07)\n", " Iteration 48 (of 50). Current convergence value = 0.000775884 (threshold = 1e-07)\n", " Iteration 49 (of 50). Current convergence value = 0.000795187 (threshold = 1e-07)\n", " Iteration 50 (of 50). Current convergence value = 0.000814762 (threshold = 1e-07)\n", " N4BiasFieldCorrectionImageFilter (0x1d226d0)\n", " RTTI typeinfo: itk::N4BiasFieldCorrectionImageFilter, itk::Image, itk::Image >\n", " Reference Count: 1\n", " Modified Time: 474\n", " Debug: Off\n", " Object Name: \n", " Observers: \n", " IterationEvent(Command)\n", " Inputs: \n", " Primary: (0x1d32400) *\n", " _1: (0x1d30b00)\n", " Indexed Inputs: \n", " 0: Primary (0x1d32400)\n", " 1: _1 (0x1d30b00)\n", " Required Input Names: Primary\n", " NumberOfRequiredInputs: 1\n", " Outputs: \n", " Primary: (0x1d29e70)\n", " Indexed Outputs: \n", " 0: Primary (0x1d29e70)\n", " NumberOfRequiredOutputs: 1\n", " Number Of Threads: 32\n", " ReleaseDataFlag: Off\n", " ReleaseDataBeforeUpdateFlag: Off\n", " AbortGenerateData: Off\n", " Progress: 0\n", " Multithreader: \n", " RTTI typeinfo: itk::PoolMultiThreader\n", " Reference Count: 1\n", " Modified Time: 138\n", " Debug: Off\n", " Object Name: \n", " Observers: \n", " none\n", " DynamicMultiThreading: On\n", " CoordinateTolerance: 1e-06\n", " DirectionTolerance: 1e-06\n", " Use Mask Label: 0\n", " Mask label: 1\n", " Number of histogram bins: 200\n", " Wiener filter noise: 0.01\n", " Bias field FWHM: 0.15\n", " Maximum number of iterations: [50, 50, 50, 50]\n", " Convergence threshold: 1e-07\n", " Spline order: 3\n", " Number of fitting levels: [4, 4, 4]\n", " Number of control points: [4, 5, 5]\n", " CurrentConvergenceMeasurement: 0.000814762\n", " CurrentLevel: 4\n", " ElapsedIterations: 51\n", " LogBiasFieldControlPointLattice: \n", " Image (0x1d2ded0)\n", " RTTI typeinfo: itk::Image, 3u>\n", " Reference Count: 1\n", " Modified Time: 396864244\n", " Debug: Off\n", " Object Name: \n", " Observers: \n", " none\n", " Source: (none)\n", " Source output name: (none)\n", " Release Data: Off\n", " Data Released: False\n", " Global Release Data: Off\n", " PipelineMTime: 0\n", " UpdateMTime: 0\n", " RealTimeStamp: 0 seconds \n", " LargestPossibleRegion: \n", " Dimension: 3\n", " Index: [0, 0, 0]\n", " Size: [11, 19, 19]\n", " BufferedRegion: \n", " Dimension: 3\n", " Index: [0, 0, 0]\n", " Size: [11, 19, 19]\n", " RequestedRegion: \n", " Dimension: 3\n", " Index: [0, 0, 0]\n", " Size: [11, 19, 19]\n", " Spacing: [24.5, 24.75, 24.75]\n", " Origin: [-24.5, 24.75, -24.75]\n", " Direction: \n", "1 0 0\n", "0 -1 0\n", "0 0 1\n", "\n", " IndexToPointMatrix: \n", "24.5 0 0\n", "0 -24.75 0\n", "0 0 24.75\n", "\n", " PointToIndexMatrix: \n", "0.0408163 0 0\n", "0 -0.040404 0\n", "0 0 0.040404\n", "\n", " Inverse Direction: \n", "1 0 0\n", "0 -1 0\n", "0 0 1\n", "\n", " PixelContainer: \n", " ImportImageContainer (0x1d2e800)\n", " RTTI typeinfo: itk::ImportImageContainer >\n", " Reference Count: 1\n", " Modified Time: 396864245\n", " Debug: Off\n", " Object Name: \n", " Observers: \n", " none\n", " Pointer: 0x1f21760\n", " Container manages memory: true\n", " Size: 3971\n", " Capacity: 3971\n", "Elapsed time: 28.2239\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "\n", "--------------------------------------------------------------------------------------\n", " Done with N4 correction (pre brain extraction): 0h 0m 41s\n", "--------------------------------------------------------------------------------------\n", "\n", "\n", "--------------------------------------------------------------------------------------\n", " Brain extraction using the following steps:\n", " 1) Register OASIS/MICCAI2012-Multi-Atlas-Challenge-Data/T_template0.nii.gz to ANTS_Stripped_N4Corrected0.nii.gz\n", " 2) Warp OASIS/MICCAI2012-Multi-Atlas-Challenge-Data/T_template0_BrainCerebellumProbabilityMask.nii.gz to ds000102/sub-08/anat/sub-08_T1w.nii.gz using, from 1),\n", " ANTS_Stripped_BrainExtractionWarp/Affine\n", " 3) Refine segmentation results using Atropos\n", "--------------------------------------------------------------------------------------\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "/opt/ants-2.3.1//ResampleImageBySpacing 3 OASIS/MICCAI2012-Multi-Atlas-Challenge-Data/T_template0.nii.gz ANTS_Stripped_BrainExtractionInitialAffineFixed.nii.gz 4 4 4 1\n", " spacing [1, 1, 1] dim 3\n", " spacing2 [4, 4, 4]\n", " smoothing by : 3 dir 0\n", " smoothing by : 3 dir 1\n", " smoothing by : 3 dir 2\n", " out space [4, 4, 4]\n", " output size [54, 64, 72] spc [4, 4, 4]\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "/opt/ants-2.3.1//ResampleImageBySpacing 3 ANTS_Stripped_N4Corrected0.nii.gz ANTS_Stripped_BrainExtractionInitialAffineMoving.nii.gz 4 4 4 1\n", " spacing [1, 1, 1] dim 3\n", " spacing2 [4, 4, 4]\n", " smoothing by : 3 dir 0\n", " smoothing by : 3 dir 1\n", " smoothing by : 3 dir 2\n", " out space [4, 4, 4]\n", " output size [44, 64, 64] spc [4, 4, 4]\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "/opt/ants-2.3.1//ImageMath 3 ANTS_Stripped_BrainExtractionLaplacian.nii.gz Laplacian ANTS_Stripped_N4Corrected0.nii.gz 1.5 1\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "/opt/ants-2.3.1//ImageMath 3 ANTS_Stripped_BrainExtractionTemplateLaplacian.nii.gz Laplacian OASIS/MICCAI2012-Multi-Atlas-Challenge-Data/T_template0.nii.gz 1.5 1\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "/opt/ants-2.3.1//antsAI -d 3 -v 1 -m Mattes[ANTS_Stripped_BrainExtractionInitialAffineFixed.nii.gz,ANTS_Stripped_BrainExtractionInitialAffineMoving.nii.gz,32,Regular,0.2] -t Affine[0.1] -s [20,0.12] -g [40,0x40x40] -p 0 -c 10 -o ANTS_Stripped_BrainExtractionInitialAffine.mat\n", "Using the Mattes MI metric (number of bins = 32)\n", "Starting optimizer with 243 starting points\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "/opt/ants-2.3.1//antsRegistration -d 3 -u 1 -w [0.025,0.975] -o ANTS_Stripped_BrainExtractionPrior -r ANTS_Stripped_BrainExtractionInitialAffine.mat -z 1 --float 0 --verbose 1 -m MI[OASIS/MICCAI2012-Multi-Atlas-Challenge-Data/T_template0.nii.gz,ANTS_Stripped_N4Corrected0.nii.gz,1,32,Regular,0.25] -c [1000x500x250x100,1e-8,10] -t Rigid[0.1] -f 8x4x2x1 -s 4x2x1x0 -m MI[OASIS/MICCAI2012-Multi-Atlas-Challenge-Data/T_template0.nii.gz,ANTS_Stripped_N4Corrected0.nii.gz,1,32,Regular,0.25] -c [1000x500x250x100,1e-8,10] -t Affine[0.1] -f 8x4x2x1 -s 4x2x1x0 -m CC[OASIS/MICCAI2012-Multi-Atlas-Challenge-Data/T_template0.nii.gz,ANTS_Stripped_N4Corrected0.nii.gz,0.5,4] -m CC[ANTS_Stripped_BrainExtractionTemplateLaplacian.nii.gz,ANTS_Stripped_BrainExtractionLaplacian.nii.gz,0.5,4] -c [50x10x0,1e-9,15] -t SyN[0.1,3,0] -f 4x2x1 -s 2x1x0\n", "All_Command_lines_OK\n", "Using double precision for computations.\n", "=============================================================================\n", "The composite transform comprises the following transforms (in order): \n", " 1. ANTS_Stripped_BrainExtractionInitialAffine.mat (type = AffineTransform)\n", "=============================================================================\n", " number of levels = 4\n", " number of levels = 4\n", " number of levels = 3\n", " fixed image: OASIS/MICCAI2012-Multi-Atlas-Challenge-Data/T_template0.nii.gz\n", " moving image: ANTS_Stripped_N4Corrected0.nii.gz\n", " fixed image: OASIS/MICCAI2012-Multi-Atlas-Challenge-Data/T_template0.nii.gz\n", " moving image: ANTS_Stripped_N4Corrected0.nii.gz\n", " fixed image: OASIS/MICCAI2012-Multi-Atlas-Challenge-Data/T_template0.nii.gz\n", " moving image: ANTS_Stripped_N4Corrected0.nii.gz\n", " fixed image: ANTS_Stripped_BrainExtractionTemplateLaplacian.nii.gz\n", " moving image: ANTS_Stripped_BrainExtractionLaplacian.nii.gz\n", "Dimension = 3\n", "Number of stages = 3\n", "Use Histogram Matching true\n", "Winsorize image intensities true\n", "Lower quantile = 0.025\n", "Upper quantile = 0.975\n", "Stage 1 State\n", " Image metric = Mattes\n", " Fixed image = Image (0x44aa3d0)\n", " RTTI typeinfo: itk::Image\n", " Reference Count: 2\n", " Modified Time: 1254\n", " Debug: Off\n", " Object Name: \n", " Observers: \n", " none\n", " Source: (none)\n", " Source output name: (none)\n", " Release Data: Off\n", " Data Released: False\n", " Global Release Data: Off\n", " PipelineMTime: 0\n", " UpdateMTime: 1065\n", " RealTimeStamp: 0 seconds \n", " LargestPossibleRegion: \n", " Dimension: 3\n", " Index: [0, 0, 0]\n", " Size: [216, 256, 291]\n", " BufferedRegion: \n", " Dimension: 3\n", " Index: [0, 0, 0]\n", " Size: [216, 256, 291]\n", " RequestedRegion: \n", " Dimension: 3\n", " Index: [0, 0, 0]\n", " Size: [216, 256, 291]\n", " Spacing: [1, 1, 1]\n", " Origin: [0, 293, 0]\n", " Direction: \n", "1 0 0\n", "0 -0 -1\n", "0 -1 -0\n", "\n", " IndexToPointMatrix: \n", "1 0 0\n", "0 0 -1\n", "0 -1 0\n", "\n", " PointToIndexMatrix: \n", "1 0 0\n", "0 0 -1\n", "0 -1 0\n", "\n", " Inverse Direction: \n", "1 0 0\n", "0 0 -1\n", "0 -1 0\n", "\n", " PixelContainer: \n", " ImportImageContainer (0x449e8d0)\n", " RTTI typeinfo: itk::ImportImageContainer\n", " Reference Count: 1\n", " Modified Time: 1062\n", " Debug: Off\n", " Object Name: \n", " Observers: \n", " none\n", " Pointer: 0x7f25a3301010\n", " Container manages memory: true\n", " Size: 16091136\n", " Capacity: 16091136\n", "\n", " Moving image = Image (0x44ad8a0)\n", " RTTI typeinfo: itk::Image\n", " Reference Count: 2\n", " Modified Time: 1255\n", " Debug: Off\n", " Object Name: \n", " Observers: \n", " none\n", " Source: (none)\n", " Source output name: (none)\n", " Release Data: Off\n", " Data Released: False\n", " Global Release Data: Off\n", " PipelineMTime: 0\n", " UpdateMTime: 1252\n", " RealTimeStamp: 0 seconds \n", " LargestPossibleRegion: \n", " Dimension: 3\n", " Index: [0, 0, 0]\n", " Size: [176, 256, 256]\n", " BufferedRegion: \n", " Dimension: 3\n", " Index: [0, 0, 0]\n", " Size: [176, 256, 256]\n", " RequestedRegion: \n", " Dimension: 3\n", " Index: [0, 0, 0]\n", " Size: [176, 256, 256]\n", " Spacing: [1, 1, 1]\n", " Origin: [0, 126.054, -133.283]\n", " Direction: \n", "1 0 0\n", "0 -1 0\n", "0 0 1\n", "\n", " IndexToPointMatrix: \n", "1 0 0\n", "0 -1 0\n", "0 0 1\n", "\n", " PointToIndexMatrix: \n", "1 0 0\n", "0 -1 0\n", "0 0 1\n", "\n", " Inverse Direction: \n", "1 0 0\n", "0 -1 0\n", "0 0 1\n", "\n", " PixelContainer: \n", " ImportImageContainer (0x449b390)\n", " RTTI typeinfo: itk::ImportImageContainer\n", " Reference Count: 1\n", " Modified Time: 1249\n", " Debug: Off\n", " Object Name: \n", " Observers: \n", " none\n", " Pointer: 0x7f259db00010\n", " Container manages memory: true\n", " Size: 11534336\n", " Capacity: 11534336\n", "\n", " Weighting = 1\n", " Sampling strategy = regular\n", " Number of bins = 32\n", " Radius = 4\n", " Sampling percentage = 0.25\n", " Transform = Rigid\n", " Gradient step = 0.1\n", " Update field sigma (voxel space) = 0\n", " Total field sigma (voxel space) = 0\n", " Update field time sigma = 0\n", " Total field time sigma = 0\n", " Number of time indices = 0\n", " Number of time point samples = 0\n", "Stage 2 State\n", " Image metric = Mattes\n", " Fixed image = Image (0x44b32c0)\n", " RTTI typeinfo: itk::Image\n", " Reference Count: 2\n", " Modified Time: 1630\n", " Debug: Off\n", " Object Name: \n", " Observers: \n", " none\n", " Source: (none)\n", " Source output name: (none)\n", " Release Data: Off\n", " Data Released: False\n", " Global Release Data: Off\n", " PipelineMTime: 0\n", " UpdateMTime: 1441\n", " RealTimeStamp: 0 seconds \n", " LargestPossibleRegion: \n", " Dimension: 3\n", " Index: [0, 0, 0]\n", " Size: [216, 256, 291]\n", " BufferedRegion: \n", " Dimension: 3\n", " Index: [0, 0, 0]\n", " Size: [216, 256, 291]\n", " RequestedRegion: \n", " Dimension: 3\n", " Index: [0, 0, 0]\n", " Size: [216, 256, 291]\n", " Spacing: [1, 1, 1]\n", " Origin: [0, 293, 0]\n", " Direction: \n", "1 0 0\n", "0 -0 -1\n", "0 -1 -0\n", "\n", " IndexToPointMatrix: \n", "1 0 0\n", "0 0 -1\n", "0 -1 0\n", "\n", " PointToIndexMatrix: \n", "1 0 0\n", "0 0 -1\n", "0 -1 0\n", "\n", " Inverse Direction: \n", "1 0 0\n", "0 0 -1\n", "0 -1 0\n", "\n", " PixelContainer: \n", " ImportImageContainer (0x44b3550)\n", " RTTI typeinfo: itk::ImportImageContainer\n", " Reference Count: 1\n", " Modified Time: 1438\n", " Debug: Off\n", " Object Name: \n", " Observers: \n", " none\n", " Pointer: 0x7f259603b010\n", " Container manages memory: true\n", " Size: 16091136\n", " Capacity: 16091136\n", "\n", " Moving image = Image (0x44b5a00)\n", " RTTI typeinfo: itk::Image\n", " Reference Count: 2\n", " Modified Time: 1631\n", " Debug: Off\n", " Object Name: \n", " Observers: \n", " none\n", " Source: (none)\n", " Source output name: (none)\n", " Release Data: Off\n", " Data Released: False\n", " Global Release Data: Off\n", " PipelineMTime: 0\n", " UpdateMTime: 1628\n", " RealTimeStamp: 0 seconds \n", " LargestPossibleRegion: \n", " Dimension: 3\n", " Index: [0, 0, 0]\n", " Size: [176, 256, 256]\n", " BufferedRegion: \n", " Dimension: 3\n", " Index: [0, 0, 0]\n", " Size: [176, 256, 256]\n", " RequestedRegion: \n", " Dimension: 3\n", " Index: [0, 0, 0]\n", " Size: [176, 256, 256]\n", " Spacing: [1, 1, 1]\n", " Origin: [0, 126.054, -133.283]\n", " Direction: \n", "1 0 0\n", "0 -1 0\n", "0 0 1\n", "\n", " IndexToPointMatrix: \n", "1 0 0\n", "0 -1 0\n", "0 0 1\n", "\n", " PointToIndexMatrix: \n", "1 0 0\n", "0 -1 0\n", "0 0 1\n", "\n", " Inverse Direction: \n", "1 0 0\n", "0 -1 0\n", "0 0 1\n", "\n", " PixelContainer: \n", " ImportImageContainer (0x44ae1d0)\n", " RTTI typeinfo: itk::ImportImageContainer\n", " Reference Count: 1\n", " Modified Time: 1625\n", " Debug: Off\n", " Object Name: \n", " Observers: \n", " none\n", " Pointer: 0x7f259083a010\n", " Container manages memory: true\n", " Size: 11534336\n", " Capacity: 11534336\n", "\n", " Weighting = 1\n", " Sampling strategy = regular\n", " Number of bins = 32\n", " Radius = 4\n", " Sampling percentage = 0.25\n", " Transform = Affine\n", " Gradient step = 0.1\n", " Update field sigma (voxel space) = 0\n", " Total field sigma (voxel space) = 0\n", " Update field time sigma = 0\n", " Total field time sigma = 0\n", " Number of time indices = 0\n", " Number of time point samples = 0\n", "Stage 3 State\n", " Image metric = CC\n", " Fixed image = Image (0x44b8b20)\n", " RTTI typeinfo: itk::Image\n", " Reference Count: 2\n", " Modified Time: 2006\n", " Debug: Off\n", " Object Name: \n", " Observers: \n", " none\n", " Source: (none)\n", " Source output name: (none)\n", " Release Data: Off\n", " Data Released: False\n", " Global Release Data: Off\n", " PipelineMTime: 0\n", " UpdateMTime: 1817\n", " RealTimeStamp: 0 seconds \n", " LargestPossibleRegion: \n", " Dimension: 3\n", " Index: [0, 0, 0]\n", " Size: [216, 256, 291]\n", " BufferedRegion: \n", " Dimension: 3\n", " Index: [0, 0, 0]\n", " Size: [216, 256, 291]\n", " RequestedRegion: \n", " Dimension: 3\n", " Index: [0, 0, 0]\n", " Size: [216, 256, 291]\n", " Spacing: [1, 1, 1]\n", " Origin: [0, 293, 0]\n", " Direction: \n", "1 0 0\n", "0 -0 -1\n", "0 -1 -0\n", "\n", " IndexToPointMatrix: \n", "1 0 0\n", "0 0 -1\n", "0 -1 0\n", "\n", " PointToIndexMatrix: \n", "1 0 0\n", "0 0 -1\n", "0 -1 0\n", "\n", " Inverse Direction: \n", "1 0 0\n", "0 0 -1\n", "0 -1 0\n", "\n", " PixelContainer: \n", " ImportImageContainer (0x44b8db0)\n", " RTTI typeinfo: itk::ImportImageContainer\n", " Reference Count: 1\n", " Modified Time: 1814\n", " Debug: Off\n", " Object Name: \n", " Observers: \n", " none\n", " Pointer: 0x7f2588d75010\n", " Container manages memory: true\n", " Size: 16091136\n", " Capacity: 16091136\n", "\n", " Moving image = Image (0x44bb1b0)\n", " RTTI typeinfo: itk::Image\n", " Reference Count: 2\n", " Modified Time: 2007\n", " Debug: Off\n", " Object Name: \n", " Observers: \n", " none\n", " Source: (none)\n", " Source output name: (none)\n", " Release Data: Off\n", " Data Released: False\n", " Global Release Data: Off\n", " PipelineMTime: 0\n", " UpdateMTime: 2004\n", " RealTimeStamp: 0 seconds \n", " LargestPossibleRegion: \n", " Dimension: 3\n", " Index: [0, 0, 0]\n", " Size: [176, 256, 256]\n", " BufferedRegion: \n", " Dimension: 3\n", " Index: [0, 0, 0]\n", " Size: [176, 256, 256]\n", " RequestedRegion: \n", " Dimension: 3\n", " Index: [0, 0, 0]\n", " Size: [176, 256, 256]\n", " Spacing: [1, 1, 1]\n", " Origin: [0, 126.054, -133.283]\n", " Direction: \n", "1 0 0\n", "0 -1 0\n", "0 0 1\n", "\n", " IndexToPointMatrix: \n", "1 0 0\n", "0 -1 0\n", "0 0 1\n", "\n", " PointToIndexMatrix: \n", "1 0 0\n", "0 -1 0\n", "0 0 1\n", "\n", " Inverse Direction: \n", "1 0 0\n", "0 -1 0\n", "0 0 1\n", "\n", " PixelContainer: \n", " ImportImageContainer (0x44bb440)\n", " RTTI typeinfo: itk::ImportImageContainer\n", " Reference Count: 1\n", " Modified Time: 2001\n", " Debug: Off\n", " Object Name: \n", " Observers: \n", " none\n", " Pointer: 0x7f2583574010\n", " Container manages memory: true\n", " Size: 11534336\n", " Capacity: 11534336\n", "\n", " Weighting = 0.5\n", " Sampling strategy = none\n", " Number of bins = 32\n", " Radius = 4\n", " Sampling percentage = 1\n", " Transform = SyN\n", " Gradient step = 0.1\n", " Update field sigma (voxel space) = 3\n", " Total field sigma (voxel space) = 0\n", " Update field time sigma = 0\n", " Total field time sigma = 0\n", " Number of time indices = 0\n", " Number of time point samples = 0\n", "Registration using 3 total stages.\n", "\n", "Stage 0\n", " iterations = 1000x500x250x100\n", " convergence threshold = 1e-08\n", " convergence window size = 10\n", " number of levels = 4\n", " using the Mattes MI metric (number of bins = 32, weight = 1)\n", " preprocessing: winsorizing the image intensities\n", " preprocessing: histogram matching the images\n", " Shrink factors (level 1 out of 4): [8, 8, 8]\n", " Shrink factors (level 2 out of 4): [4, 4, 4]\n", " Shrink factors (level 3 out of 4): [2, 2, 2]\n", " Shrink factors (level 4 out of 4): [1, 1, 1]\n", " smoothing sigmas per level: [4, 2, 1, 0]\n", " regular sampling (percentage = 0.25)\n", "\n", "*** Running Euler3DTransform registration ***\n", "\n", "DIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST\n", " 2DIAGNOSTIC, 1, -7.453514267733e-01, 1.797693134862e+308, 1.5526e+00, 1.5526e+00, \n", " 2DIAGNOSTIC, 2, -7.456931743917e-01, 1.797693134862e+308, 1.5563e+00, 3.6461e-03, \n", " 2DIAGNOSTIC, 3, -7.460062709731e-01, 1.797693134862e+308, 1.5600e+00, 3.7551e-03, \n", " 2DIAGNOSTIC, 4, -7.463763212183e-01, 1.797693134862e+308, 1.5634e+00, 3.3910e-03, \n", " 2DIAGNOSTIC, 5, -7.467015173865e-01, 1.797693134862e+308, 1.5669e+00, 3.4730e-03, \n", " 2DIAGNOSTIC, 6, -7.473843848417e-01, 1.797693134862e+308, 1.5703e+00, 3.4220e-03, \n", " 2DIAGNOSTIC, 7, -7.481396381420e-01, 1.797693134862e+308, 1.5737e+00, 3.4039e-03, \n", " 2DIAGNOSTIC, 8, -7.492428219049e-01, 1.797693134862e+308, 1.5784e+00, 4.6759e-03, \n", " 2DIAGNOSTIC, 9, -7.496987116603e-01, 1.797693134862e+308, 1.5831e+00, 4.7190e-03, \n", " 2DIAGNOSTIC, 10, -7.502117933270e-01, 4.430288860050e-04, 1.5945e+00, 1.1403e-02, \n", " 2DIAGNOSTIC, 11, -7.501096126970e-01, 4.083670252657e-04, 1.6003e+00, 5.7881e-03, \n", " 2DIAGNOSTIC, 12, -7.512639492123e-01, 3.904095527388e-04, 1.6076e+00, 7.2992e-03, \n", " 2DIAGNOSTIC, 13, -7.512578402002e-01, 3.478939170554e-04, 1.6126e+00, 5.0051e-03, \n", " 2DIAGNOSTIC, 14, -7.511130974570e-01, 2.864905402189e-04, 1.6184e+00, 5.7900e-03, \n", " 2DIAGNOSTIC, 15, -7.510984264701e-01, 2.157366113679e-04, 1.6233e+00, 4.9250e-03, \n", " 2DIAGNOSTIC, 16, -7.510290124070e-01, 1.486595042399e-04, 1.6282e+00, 4.8320e-03, \n", " 2DIAGNOSTIC, 17, -7.510281692651e-01, 9.200238827316e-05, 1.6330e+00, 4.8618e-03, \n", " 2DIAGNOSTIC, 18, -7.510915605334e-01, 5.764285079444e-05, 1.6379e+00, 4.9088e-03, \n", " 2DIAGNOSTIC, 19, -7.511811758409e-01, 3.267356885803e-05, 1.6423e+00, 4.3330e-03, \n", " 2DIAGNOSTIC, 20, -7.515272067869e-01, 2.392430803864e-05, 1.6471e+00, 4.8242e-03, \n", " 2DIAGNOSTIC, 21, -7.516202807758e-01, 1.300597376754e-05, 1.6514e+00, 4.2992e-03, \n", " 2DIAGNOSTIC, 22, -7.518438624048e-01, 2.578137546857e-05, 1.6569e+00, 5.5709e-03, \n", " 2DIAGNOSTIC, 23, -7.519081498530e-01, 3.615500306312e-05, 1.6619e+00, 4.9670e-03, \n", " 2DIAGNOSTIC, 24, -7.518342864874e-01, 3.893247878763e-05, 1.6661e+00, 4.2250e-03, \n", " 2DIAGNOSTIC, 25, -7.519942728735e-01, 4.020519198113e-05, 1.6702e+00, 4.1008e-03, \n", " 2DIAGNOSTIC, 26, -7.520878045734e-01, 3.798434544184e-05, 1.6744e+00, 4.1401e-03, \n", " 2DIAGNOSTIC, 27, -7.522893157208e-01, 3.526289315513e-05, 1.6793e+00, 4.8871e-03, \n", " 2DIAGNOSTIC, 28, -7.525984792176e-01, 3.455571985873e-05, 1.6843e+00, 4.9999e-03, \n", " 2DIAGNOSTIC, 29, -7.527042730235e-01, 3.316866515075e-05, 1.6898e+00, 5.5211e-03, \n", " 2DIAGNOSTIC, 30, -7.526829783699e-01, 3.297205443902e-05, 1.6950e+00, 5.1680e-03, \n", " 2DIAGNOSTIC, 31, -7.527000925386e-01, 3.107947274942e-05, 1.7024e+00, 7.4000e-03, \n", " 2DIAGNOSTIC, 32, -7.528560535731e-01, 3.090221735819e-05, 1.7083e+00, 5.9440e-03, \n", " 2DIAGNOSTIC, 33, -7.530047938638e-01, 3.028201611617e-05, 1.7135e+00, 5.2390e-03, \n", " 2DIAGNOSTIC, 34, -7.529558688988e-01, 2.549090116167e-05, 1.7180e+00, 4.4849e-03, \n", " 2DIAGNOSTIC, 35, -7.532200968914e-01, 2.334324413653e-05, 1.7227e+00, 4.6339e-03, \n", " 2DIAGNOSTIC, 36, -7.535276642011e-01, 2.332813366595e-05, 1.7273e+00, 4.6189e-03, \n", " 2DIAGNOSTIC, 37, -7.539589564141e-01, 2.747186362147e-05, 1.7318e+00, 4.4761e-03, \n", " 2DIAGNOSTIC, 38, -7.545048501387e-01, 3.727657598369e-05, 1.7363e+00, 4.5450e-03, \n", " 2DIAGNOSTIC, 39, -7.553594420989e-01, 5.239463028742e-05, 1.7413e+00, 4.9632e-03, \n", " 2DIAGNOSTIC, 40, -7.576594988225e-01, 8.326572049852e-05, 1.7475e+00, 6.2730e-03, \n", " 2DIAGNOSTIC, 41, -7.581277284084e-01, 1.086924208943e-04, 1.7573e+00, 9.7940e-03, \n", " 2DIAGNOSTIC, 42, -7.582370739064e-01, 1.251392899489e-04, 1.7713e+00, 1.3990e-02, \n", " 2DIAGNOSTIC, 43, -7.584967112831e-01, 1.328365347707e-04, 1.7799e+00, 8.6248e-03, \n", " 2DIAGNOSTIC, 44, -7.584100562432e-01, 1.262164820983e-04, 1.7862e+00, 6.2251e-03, \n", " 2DIAGNOSTIC, 45, -7.584279268765e-01, 1.100018358416e-04, 1.7914e+00, 5.1980e-03, \n", " 2DIAGNOSTIC, 46, -7.583776629334e-01, 8.610584246393e-05, 1.7960e+00, 4.6091e-03, \n", " 2DIAGNOSTIC, 47, -7.583401370875e-01, 5.844903562423e-05, 1.8004e+00, 4.4680e-03, \n", " 2DIAGNOSTIC, 48, -7.583132354545e-01, 3.056271743384e-05, 1.8056e+00, 5.1479e-03, \n", " 2DIAGNOSTIC, 49, -7.584188215673e-01, 7.908599722887e-06, 1.8108e+00, 5.1839e-03, \n", " 2DIAGNOSTIC, 50, -7.582456000328e-01, 1.448006575665e-06, 1.8159e+00, 5.1410e-03, \n", "DIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST\n", " 2DIAGNOSTIC, 1, -5.953725090995e-01, 1.797693134862e+308, 3.4988e+00, 1.6828e+00, \n", " 2DIAGNOSTIC, 2, -5.955236821794e-01, 1.797693134862e+308, 3.5274e+00, 2.8602e-02, \n", " 2DIAGNOSTIC, 3, -5.957095372059e-01, 1.797693134862e+308, 3.5526e+00, 2.5274e-02, \n", " 2DIAGNOSTIC, 4, -5.958233285972e-01, 1.797693134862e+308, 3.5731e+00, 2.0457e-02, \n", " 2DIAGNOSTIC, 5, -5.961740133405e-01, 1.797693134862e+308, 3.5952e+00, 2.2073e-02, \n", " 2DIAGNOSTIC, 6, -5.977483335188e-01, 1.797693134862e+308, 3.6247e+00, 2.9552e-02, \n", " 2DIAGNOSTIC, 7, -5.981171879932e-01, 1.797693134862e+308, 3.6497e+00, 2.4954e-02, \n", " 2DIAGNOSTIC, 8, -5.985344943869e-01, 1.797693134862e+308, 3.6794e+00, 2.9727e-02, \n", " 2DIAGNOSTIC, 9, -5.992720284232e-01, 1.797693134862e+308, 3.6995e+00, 2.0145e-02, \n", " 2DIAGNOSTIC, 10, -5.996349951048e-01, 5.196154602357e-04, 3.7448e+00, 4.5297e-02, \n", " 2DIAGNOSTIC, 11, -5.997482463710e-01, 4.889194391473e-04, 3.7667e+00, 2.1887e-02, \n", " 2DIAGNOSTIC, 12, -6.000231158923e-01, 4.367084547312e-04, 3.7890e+00, 2.2260e-02, \n", " 2DIAGNOSTIC, 13, -6.002454744020e-01, 3.688416926905e-04, 3.8146e+00, 2.5612e-02, \n", " 2DIAGNOSTIC, 14, -6.004717953466e-01, 2.889198494387e-04, 3.8381e+00, 2.3527e-02, \n", " 2DIAGNOSTIC, 15, -6.008332065469e-01, 2.147323516626e-04, 3.8585e+00, 2.0378e-02, \n", " 2DIAGNOSTIC, 16, -6.028209459581e-01, 2.360015449458e-04, 3.8915e+00, 3.3007e-02, \n", " 2DIAGNOSTIC, 17, -6.031961154976e-01, 2.525346714568e-04, 3.9388e+00, 4.7279e-02, \n", " 2DIAGNOSTIC, 18, -6.031822061908e-01, 2.546666825495e-04, 3.9644e+00, 2.5659e-02, \n", " 2DIAGNOSTIC, 19, -6.032299679687e-01, 2.534160031031e-04, 3.9913e+00, 2.6879e-02, \n", " 2DIAGNOSTIC, 20, -6.032401527082e-01, 2.376066809194e-04, 4.0123e+00, 2.0952e-02, \n", " 2DIAGNOSTIC, 21, -6.032461641407e-01, 2.031727399052e-04, 4.0370e+00, 2.4727e-02, \n", " 2DIAGNOSTIC, 22, -6.032511147610e-01, 1.588594058269e-04, 4.0617e+00, 2.4647e-02, \n", " 2DIAGNOSTIC, 23, -6.032527014742e-01, 1.089076500706e-04, 4.0857e+00, 2.4034e-02, \n", " 2DIAGNOSTIC, 24, -6.032588373865e-01, 5.802740495668e-05, 4.1153e+00, 2.9567e-02, \n", " 2DIAGNOSTIC, 25, -6.032673040442e-01, 1.191444589613e-05, 4.1423e+00, 2.7055e-02, \n", " 2DIAGNOSTIC, 26, -6.032745023667e-01, 4.500987750081e-06, 4.1710e+00, 2.8648e-02, \n", " 2DIAGNOSTIC, 27, -6.032682735511e-01, 3.817113198065e-06, 4.1959e+00, 2.4953e-02, \n", " 2DIAGNOSTIC, 28, -6.032735735132e-01, 2.774671915229e-06, 4.2223e+00, 2.6355e-02, \n", " 2DIAGNOSTIC, 29, -6.032690618315e-01, 2.349551592465e-06, 4.2407e+00, 1.8418e-02, \n", " 2DIAGNOSTIC, 30, -6.032640294824e-01, 1.913209286664e-06, 4.2614e+00, 2.0720e-02, \n", " 2DIAGNOSTIC, 31, -6.032752952233e-01, 1.688832420813e-06, 4.2795e+00, 1.8120e-02, \n", " 2DIAGNOSTIC, 32, -6.032948792009e-01, 1.775352833369e-06, 4.3005e+00, 2.1014e-02, \n", " 2DIAGNOSTIC, 33, -6.033162053151e-01, 2.103910057137e-06, 4.3213e+00, 2.0720e-02, \n", " 2DIAGNOSTIC, 34, -6.033672171695e-01, 3.094807632852e-06, 4.3384e+00, 1.7138e-02, \n", " 2DIAGNOSTIC, 35, -6.034525524496e-01, 5.077430358890e-06, 4.3568e+00, 1.8435e-02, \n", " 2DIAGNOSTIC, 36, -6.035710823408e-01, 8.184044928243e-06, 4.3766e+00, 1.9792e-02, \n", " 2DIAGNOSTIC, 37, -6.036543227937e-01, 1.138248248355e-05, 4.3945e+00, 1.7874e-02, \n", " 2DIAGNOSTIC, 38, -6.037578078861e-01, 1.476396085648e-05, 4.4164e+00, 2.1906e-02, \n", " 2DIAGNOSTIC, 39, -6.040840337747e-01, 2.053430965986e-05, 4.4369e+00, 2.0503e-02, \n", " 2DIAGNOSTIC, 40, -6.044101093967e-01, 2.782613242658e-05, 4.4626e+00, 2.5675e-02, \n", " 2DIAGNOSTIC, 41, -6.047009125946e-01, 3.559516415582e-05, 4.5001e+00, 3.7483e-02, \n", " 2DIAGNOSTIC, 42, -6.048787563353e-01, 4.188961577632e-05, 4.5183e+00, 1.8197e-02, \n", " 2DIAGNOSTIC, 43, -6.048042969817e-01, 4.339863888258e-05, 4.5363e+00, 1.8024e-02, \n", " 2DIAGNOSTIC, 44, -6.048874610921e-01, 4.222576955942e-05, 4.5554e+00, 1.9136e-02, \n", " 2DIAGNOSTIC, 45, -6.054773265361e-01, 4.412791406360e-05, 4.5779e+00, 2.2433e-02, \n", " 2DIAGNOSTIC, 46, -6.070905090567e-01, 5.936214055808e-05, 4.6000e+00, 2.2162e-02, \n", " 2DIAGNOSTIC, 47, -6.076297659175e-01, 7.422451824883e-05, 4.6221e+00, 2.2129e-02, \n", " 2DIAGNOSTIC, 48, -6.079646877291e-01, 8.585916180670e-05, 4.6683e+00, 4.6180e-02, \n", " 2DIAGNOSTIC, 49, -6.079172217675e-01, 9.170072045305e-05, 4.6884e+00, 2.0113e-02, \n", " 2DIAGNOSTIC, 50, -6.079250371394e-01, 9.164071734094e-05, 4.7087e+00, 2.0229e-02, \n", " 2DIAGNOSTIC, 51, -6.079348616256e-01, 8.534785688390e-05, 4.7372e+00, 2.8499e-02, \n", " 2DIAGNOSTIC, 52, -6.079296199079e-01, 7.269665707593e-05, 4.7640e+00, 2.6874e-02, \n", " 2DIAGNOSTIC, 53, -6.079754539594e-01, 5.356888291580e-05, 4.7908e+00, 2.6809e-02, \n", " 2DIAGNOSTIC, 54, -6.079624039955e-01, 3.076793827739e-05, 4.8237e+00, 3.2844e-02, \n", " 2DIAGNOSTIC, 55, -6.079674953891e-01, 1.071817711864e-05, 4.8524e+00, 2.8686e-02, \n", " 2DIAGNOSTIC, 56, -6.079403594612e-01, 3.665212660552e-06, 4.8770e+00, 2.4577e-02, \n", " 2DIAGNOSTIC, 57, -6.079364517427e-01, 9.116550091469e-07, 4.9003e+00, 2.3333e-02, \n", " 2DIAGNOSTIC, 58, -6.079266624356e-01, 8.679183807238e-07, 4.9249e+00, 2.4662e-02, \n", " 2DIAGNOSTIC, 59, -6.079235100924e-01, 3.882125471505e-07, 4.9505e+00, 2.5581e-02, \n", "DIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST\n", " 2DIAGNOSTIC, 1, -5.266830066596e-01, 1.797693134862e+308, 6.1522e+00, 1.2017e+00, \n", " 2DIAGNOSTIC, 2, -5.268974184243e-01, 1.797693134862e+308, 6.2913e+00, 1.3915e-01, \n", " 2DIAGNOSTIC, 3, -5.269209825279e-01, 1.797693134862e+308, 6.4555e+00, 1.6417e-01, \n", " 2DIAGNOSTIC, 4, -5.269289888951e-01, 1.797693134862e+308, 6.6191e+00, 1.6357e-01, \n", " 2DIAGNOSTIC, 5, -5.269251779420e-01, 1.797693134862e+308, 6.7840e+00, 1.6493e-01, \n", " 2DIAGNOSTIC, 6, -5.269232390517e-01, 1.797693134862e+308, 6.9802e+00, 1.9622e-01, \n", " 2DIAGNOSTIC, 7, -5.269232555812e-01, 1.797693134862e+308, 7.1312e+00, 1.5099e-01, \n", " 2DIAGNOSTIC, 8, -5.269216095995e-01, 1.797693134862e+308, 7.2648e+00, 1.3360e-01, \n", " 2DIAGNOSTIC, 9, -5.269210882585e-01, 1.797693134862e+308, 7.4469e+00, 1.8212e-01, \n", " 2DIAGNOSTIC, 10, -5.269205711018e-01, 1.697289615152e-05, 7.5986e+00, 1.5171e-01, \n", " 2DIAGNOSTIC, 11, -5.269194592797e-01, 3.601516782178e-06, 7.7491e+00, 1.5048e-01, \n", " 2DIAGNOSTIC, 12, -5.269183405537e-01, 1.955226251460e-06, 7.8816e+00, 1.3253e-01, \n", " 2DIAGNOSTIC, 13, -5.269183285548e-01, 1.591170720502e-06, 8.0191e+00, 1.3743e-01, \n", " 2DIAGNOSTIC, 14, -5.269183579690e-01, 1.669233046994e-06, 8.1984e+00, 1.7932e-01, \n", " 2DIAGNOSTIC, 15, -5.269188896610e-01, 1.674897006088e-06, 8.3572e+00, 1.5885e-01, \n", " 2DIAGNOSTIC, 16, -5.269183262747e-01, 1.635739993608e-06, 8.4984e+00, 1.4118e-01, \n", " 2DIAGNOSTIC, 17, -5.269172661919e-01, 1.603018714283e-06, 8.6682e+00, 1.6982e-01, \n", " 2DIAGNOSTIC, 18, -5.269172777620e-01, 1.550543465866e-06, 8.8017e+00, 1.3342e-01, \n", " 2DIAGNOSTIC, 19, -5.269167689061e-01, 1.493248668508e-06, 8.9433e+00, 1.4165e-01, \n", " 2DIAGNOSTIC, 20, -5.269167632511e-01, 1.444635459591e-06, 9.0788e+00, 1.3553e-01, \n", " 2DIAGNOSTIC, 21, -5.269168608112e-01, 1.389170639375e-06, 9.2283e+00, 1.4946e-01, \n", " 2DIAGNOSTIC, 22, -5.269157173656e-01, 1.295459866595e-06, 9.3876e+00, 1.5929e-01, \n", " 2DIAGNOSTIC, 23, -5.269152115600e-01, 1.212674424877e-06, 9.5409e+00, 1.5329e-01, \n", " 2DIAGNOSTIC, 24, -5.269147508158e-01, 1.142425845924e-06, 9.6834e+00, 1.4249e-01, \n", " 2DIAGNOSTIC, 25, -5.269136730772e-01, 1.083064621960e-06, 9.8126e+00, 1.2919e-01, \n", " 2DIAGNOSTIC, 26, -5.269136748660e-01, 1.035297837869e-06, 9.9629e+00, 1.5033e-01, \n", " 2DIAGNOSTIC, 27, -5.269131436619e-01, 9.768789557413e-07, 1.0103e+01, 1.4014e-01, \n", " 2DIAGNOSTIC, 28, -5.269141934412e-01, 9.626082480632e-07, 1.0249e+01, 1.4601e-01, \n", " 2DIAGNOSTIC, 29, -5.269147721682e-01, 9.662603392899e-07, 1.0374e+01, 1.2468e-01, \n", " 2DIAGNOSTIC, 30, -5.269126144939e-01, 9.428130039943e-07, 1.0530e+01, 1.5607e-01, \n", " 2DIAGNOSTIC, 31, -5.269115769474e-01, 9.175798452998e-07, 1.0669e+01, 1.3944e-01, \n", " 2DIAGNOSTIC, 32, -5.269120908840e-01, 8.937585196031e-07, 1.0874e+01, 2.0454e-01, \n", " 2DIAGNOSTIC, 33, -5.269115507993e-01, 8.624926533460e-07, 1.1013e+01, 1.3890e-01, \n", " 2DIAGNOSTIC, 34, -5.269099643589e-01, 8.105607156618e-07, 1.1134e+01, 1.2098e-01, \n", " 2DIAGNOSTIC, 35, -5.269083335339e-01, 7.332153254130e-07, 1.1279e+01, 1.4519e-01, \n", " 2DIAGNOSTIC, 36, -5.269083475064e-01, 6.783007152761e-07, 1.1404e+01, 1.2525e-01, \n", " 2DIAGNOSTIC, 37, -5.269077762367e-01, 6.282630781451e-07, 1.1558e+01, 1.5357e-01, \n", " 2DIAGNOSTIC, 38, -5.269072796256e-01, 6.099545592775e-07, 1.1685e+01, 1.2763e-01, \n", " 2DIAGNOSTIC, 39, -5.269067957598e-01, 6.169321286956e-07, 1.1837e+01, 1.5186e-01, \n", " 2DIAGNOSTIC, 40, -5.269079533606e-01, 6.298216782587e-07, 1.1984e+01, 1.4694e-01, \n", " 2DIAGNOSTIC, 41, -5.269074353168e-01, 6.362711082938e-07, 1.2158e+01, 1.7349e-01, \n", " 2DIAGNOSTIC, 42, -5.269069002861e-01, 6.554973240105e-07, 1.2310e+01, 1.5251e-01, \n", " 2DIAGNOSTIC, 43, -5.269047738035e-01, 6.509467879862e-07, 1.2462e+01, 1.5195e-01, \n", " 2DIAGNOSTIC, 44, -5.269037119615e-01, 6.237222445922e-07, 1.2623e+01, 1.6071e-01, \n", " 2DIAGNOSTIC, 45, -5.269030853711e-01, 5.797187723651e-07, 1.2769e+01, 1.4590e-01, \n", " 2DIAGNOSTIC, 46, -5.269020047303e-01, 5.370474806358e-07, 1.2919e+01, 1.4993e-01, \n", " 2DIAGNOSTIC, 47, -5.269009920030e-01, 4.934019001042e-07, 1.3071e+01, 1.5205e-01, \n", " 2DIAGNOSTIC, 48, -5.269004948402e-01, 4.587257947906e-07, 1.3221e+01, 1.5018e-01, \n", " 2DIAGNOSTIC, 49, -5.268999305631e-01, 4.330808985147e-07, 1.3354e+01, 1.3327e-01, \n", " 2DIAGNOSTIC, 50, -5.268993788456e-01, 4.355614764105e-07, 1.3539e+01, 1.8481e-01, \n", " 2DIAGNOSTIC, 51, -5.268988396127e-01, 4.459777506217e-07, 1.3688e+01, 1.4893e-01, \n", " 2DIAGNOSTIC, 52, -5.268983291457e-01, 4.628278917687e-07, 1.3814e+01, 1.2659e-01, \n", " 2DIAGNOSTIC, 53, -5.268978335170e-01, 4.668359376292e-07, 1.3978e+01, 1.6345e-01, \n", " 2DIAGNOSTIC, 54, -5.268972811941e-01, 4.673847078494e-07, 1.4125e+01, 1.4740e-01, \n", " 2DIAGNOSTIC, 55, -5.268972817114e-01, 4.737104305937e-07, 1.4253e+01, 1.2750e-01, \n", " 2DIAGNOSTIC, 56, -5.268967341648e-01, 4.742978928114e-07, 1.4412e+01, 1.5892e-01, \n", " 2DIAGNOSTIC, 57, -5.268946180238e-01, 4.544307050311e-07, 1.4587e+01, 1.7576e-01, \n", " 2DIAGNOSTIC, 58, -5.268946181430e-01, 4.412109311756e-07, 1.4747e+01, 1.5950e-01, \n", " 2DIAGNOSTIC, 59, -5.268940947018e-01, 4.286023246938e-07, 1.4911e+01, 1.6397e-01, \n", " 2DIAGNOSTIC, 60, -5.268930263767e-01, 4.123550532698e-07, 1.5071e+01, 1.6047e-01, \n", " 2DIAGNOSTIC, 61, -5.268924297998e-01, 3.982943097766e-07, 1.5227e+01, 1.5519e-01, \n", " 2DIAGNOSTIC, 62, -5.268913931524e-01, 3.834375009275e-07, 1.5399e+01, 1.7256e-01, \n", " 2DIAGNOSTIC, 63, -5.268908167460e-01, 3.725382580165e-07, 1.5544e+01, 1.4488e-01, \n", " 2DIAGNOSTIC, 64, -5.268892116109e-01, 3.562557039372e-07, 1.5694e+01, 1.5026e-01, \n", " 2DIAGNOSTIC, 65, -5.268881278074e-01, 3.453278541177e-07, 1.5813e+01, 1.1855e-01, \n", " 2DIAGNOSTIC, 66, -5.268873783556e-01, 3.385991729325e-07, 1.5970e+01, 1.5758e-01, \n", " 2DIAGNOSTIC, 67, -5.268863229226e-01, 3.201932991075e-07, 1.6128e+01, 1.5796e-01, \n", " 2DIAGNOSTIC, 68, -5.268857658058e-01, 3.129306954466e-07, 1.6263e+01, 1.3484e-01, \n", " 2DIAGNOSTIC, 69, -5.268841858036e-01, 3.046039131170e-07, 1.6409e+01, 1.4566e-01, \n", " 2DIAGNOSTIC, 70, -5.268842336372e-01, 3.040666483305e-07, 1.6579e+01, 1.6984e-01, \n", " 2DIAGNOSTIC, 71, -5.268853022081e-01, 3.215362703451e-07, 1.6758e+01, 1.7958e-01, \n", " 2DIAGNOSTIC, 72, -5.268836857804e-01, 3.304437340805e-07, 1.6929e+01, 1.7051e-01, \n", " 2DIAGNOSTIC, 73, -5.268836782226e-01, 3.462727142991e-07, 1.7203e+01, 2.7386e-01, \n", " 2DIAGNOSTIC, 74, -5.268831369795e-01, 3.548914810220e-07, 1.7370e+01, 1.6745e-01, \n", " 2DIAGNOSTIC, 75, -5.268836545512e-01, 3.663689590264e-07, 1.7520e+01, 1.4990e-01, \n", " 2DIAGNOSTIC, 76, -5.268825905769e-01, 3.699946819063e-07, 1.7667e+01, 1.4703e-01, \n", " 2DIAGNOSTIC, 77, -5.268819986972e-01, 3.670151026043e-07, 1.7808e+01, 1.4094e-01, \n", " 2DIAGNOSTIC, 78, -5.268814618180e-01, 3.615784723160e-07, 1.7954e+01, 1.4646e-01, \n", " 2DIAGNOSTIC, 79, -5.268820471028e-01, 3.538374318147e-07, 1.8167e+01, 2.1289e-01, \n", " 2DIAGNOSTIC, 80, -5.268825799646e-01, 3.543408298896e-07, 1.8349e+01, 1.8212e-01, \n", " 2DIAGNOSTIC, 81, -5.268803776436e-01, 3.517205212841e-07, 1.8511e+01, 1.6168e-01, \n", " 2DIAGNOSTIC, 82, -5.268804326487e-01, 3.434911320238e-07, 1.8700e+01, 1.8853e-01, \n", " 2DIAGNOSTIC, 83, -5.268809284448e-01, 3.428869774728e-07, 1.8890e+01, 1.9076e-01, \n", " 2DIAGNOSTIC, 84, -5.268805085159e-01, 3.394048767261e-07, 1.9050e+01, 1.5923e-01, \n", " 2DIAGNOSTIC, 85, -5.268805267276e-01, 3.433950590999e-07, 1.9206e+01, 1.5623e-01, \n", " 2DIAGNOSTIC, 86, -5.268806158526e-01, 3.445187338746e-07, 1.9390e+01, 1.8458e-01, \n", " 2DIAGNOSTIC, 87, -5.268807062211e-01, 3.451286119532e-07, 1.9636e+01, 2.4575e-01, \n", " 2DIAGNOSTIC, 88, -5.268807142220e-01, 3.441303071602e-07, 1.9793e+01, 1.5716e-01, \n", " 2DIAGNOSTIC, 89, -5.268796274410e-01, 3.415888097068e-07, 1.9928e+01, 1.3479e-01, \n", " 2DIAGNOSTIC, 90, -5.268790861108e-01, 3.412150637871e-07, 2.0089e+01, 1.6079e-01, \n", " 2DIAGNOSTIC, 91, -5.268785258796e-01, 3.256455024542e-07, 2.0217e+01, 1.2837e-01, \n", " 2DIAGNOSTIC, 92, -5.268779714372e-01, 3.096282552642e-07, 2.0365e+01, 1.4745e-01, \n", " 2DIAGNOSTIC, 93, -5.268779905151e-01, 3.005389318869e-07, 2.0526e+01, 1.6095e-01, \n", " 2DIAGNOSTIC, 94, -5.268779792297e-01, 2.932182445181e-07, 2.0680e+01, 1.5383e-01, \n", " 2DIAGNOSTIC, 95, -5.268779505058e-01, 2.903953070198e-07, 2.0819e+01, 1.3989e-01, \n", " 2DIAGNOSTIC, 96, -5.268774495449e-01, 2.895865230685e-07, 2.0945e+01, 1.2552e-01, \n", " 2DIAGNOSTIC, 97, -5.268769082124e-01, 2.903456916455e-07, 2.1092e+01, 1.4670e-01, \n", " 2DIAGNOSTIC, 98, -5.268763805484e-01, 2.920122232561e-07, 2.1222e+01, 1.3084e-01, \n", " 2DIAGNOSTIC, 99, -5.268758610389e-01, 2.880485630227e-07, 2.1375e+01, 1.5293e-01, \n", " 2DIAGNOSTIC, 100, -5.268758977108e-01, 2.847255541494e-07, 2.1528e+01, 1.5230e-01, \n", " 2DIAGNOSTIC, 101, -5.268759218443e-01, 2.818929845400e-07, 2.1682e+01, 1.5453e-01, \n", " 2DIAGNOSTIC, 102, -5.268753472580e-01, 2.763626058642e-07, 2.1832e+01, 1.4946e-01, \n", " 2DIAGNOSTIC, 103, -5.268748404542e-01, 2.719383310253e-07, 2.1980e+01, 1.4798e-01, \n", " 2DIAGNOSTIC, 104, -5.268742684509e-01, 2.681705679065e-07, 2.2128e+01, 1.4878e-01, \n", " 2DIAGNOSTIC, 105, -5.268718974563e-01, 2.558050606252e-07, 2.2269e+01, 1.4032e-01, \n", " 2DIAGNOSTIC, 106, -5.268725046366e-01, 2.490598546498e-07, 2.2424e+01, 1.5562e-01, \n", " 2DIAGNOSTIC, 107, -5.268720205710e-01, 2.420428744827e-07, 2.2568e+01, 1.4390e-01, \n", " 2DIAGNOSTIC, 108, -5.268725415196e-01, 2.405303045246e-07, 2.2725e+01, 1.5709e-01, \n", " 2DIAGNOSTIC, 109, -5.268719946955e-01, 2.389992275423e-07, 2.2879e+01, 1.5345e-01, \n", " 2DIAGNOSTIC, 110, -5.268731151993e-01, 2.484763084697e-07, 2.3004e+01, 1.2475e-01, \n", " 2DIAGNOSTIC, 111, -5.268743295445e-01, 2.676063420009e-07, 2.3159e+01, 1.5569e-01, \n", " 2DIAGNOSTIC, 112, -5.268755052464e-01, 2.908516395870e-07, 2.3284e+01, 1.2425e-01, \n", " 2DIAGNOSTIC, 113, -5.268850381708e-01, 3.560684174436e-07, 2.3529e+01, 2.4552e-01, \n", " 2DIAGNOSTIC, 114, -5.268841977593e-01, 4.054320204526e-07, 2.3691e+01, 1.6146e-01, \n", " 2DIAGNOSTIC, 115, -5.268842004215e-01, 4.311431961532e-07, 2.3851e+01, 1.6069e-01, \n", " 2DIAGNOSTIC, 116, -5.268831369819e-01, 4.398954857546e-07, 2.3974e+01, 1.2239e-01, \n", " 2DIAGNOSTIC, 117, -5.268884284057e-01, 4.543773801484e-07, 2.4124e+01, 1.5082e-01, \n", " 2DIAGNOSTIC, 118, -5.268879239284e-01, 4.497223802056e-07, 2.4292e+01, 1.6806e-01, \n", " 2DIAGNOSTIC, 119, -5.268873270871e-01, 4.226733208417e-07, 2.4438e+01, 1.4569e-01, \n", " 2DIAGNOSTIC, 120, -5.268861519222e-01, 3.818342621757e-07, 2.4562e+01, 1.2405e-01, \n", " 2DIAGNOSTIC, 121, -5.268861814552e-01, 3.362624244174e-07, 2.4708e+01, 1.4592e-01, \n", " 2DIAGNOSTIC, 122, -5.268869585640e-01, 2.912221289762e-07, 2.4858e+01, 1.4977e-01, \n", " 2DIAGNOSTIC, 123, -5.268864560218e-01, 2.833682030117e-07, 2.4993e+01, 1.3471e-01, \n", " 2DIAGNOSTIC, 124, -5.268854277990e-01, 2.656065986734e-07, 2.5148e+01, 1.5584e-01, \n", " 2DIAGNOSTIC, 125, -5.268849415699e-01, 2.457832286029e-07, 2.5303e+01, 1.5500e-01, \n", " 2DIAGNOSTIC, 126, -5.268843933665e-01, 2.194769350653e-07, 2.5419e+01, 1.1531e-01, \n", " 2DIAGNOSTIC, 127, -5.268815098099e-01, 2.068847519219e-07, 2.5562e+01, 1.4276e-01, \n", " 2DIAGNOSTIC, 128, -5.268821892124e-01, 1.997965275828e-07, 2.5716e+01, 1.5443e-01, \n", " 2DIAGNOSTIC, 129, -5.268823136758e-01, 1.955906254077e-07, 2.5858e+01, 1.4204e-01, \n", " 2DIAGNOSTIC, 130, -5.268821972740e-01, 1.909240491590e-07, 2.6004e+01, 1.4617e-01, \n", " 2DIAGNOSTIC, 131, -5.268834661613e-01, 1.968635952934e-07, 2.6187e+01, 1.8249e-01, \n", " 2DIAGNOSTIC, 132, -5.268813814670e-01, 2.018580529881e-07, 2.6326e+01, 1.3955e-01, \n", " 2DIAGNOSTIC, 133, -5.268812594993e-01, 2.083937338509e-07, 2.6468e+01, 1.4163e-01, \n", " 2DIAGNOSTIC, 134, -5.268812678600e-01, 2.135336017433e-07, 2.6580e+01, 1.1208e-01, \n", " 2DIAGNOSTIC, 135, -5.268807720481e-01, 2.168015065321e-07, 2.6740e+01, 1.5972e-01, \n", " 2DIAGNOSTIC, 136, -5.268823791490e-01, 2.264138457154e-07, 2.6881e+01, 1.4126e-01, \n", " 2DIAGNOSTIC, 137, -5.268823447227e-01, 2.249622541948e-07, 2.7026e+01, 1.4521e-01, \n", " 2DIAGNOSTIC, 138, -5.268823738930e-01, 2.271506144161e-07, 2.7163e+01, 1.3680e-01, \n", " 2DIAGNOSTIC, 139, -5.268818426565e-01, 2.281001856537e-07, 2.7291e+01, 1.2849e-01, \n", " 2DIAGNOSTIC, 140, -5.268799853542e-01, 2.213259570529e-07, 2.7422e+01, 1.3026e-01, \n", " 2DIAGNOSTIC, 141, -5.268815844540e-01, 2.264987980331e-07, 2.7569e+01, 1.4714e-01, \n", " 2DIAGNOSTIC, 142, -5.268821605251e-01, 2.254506365389e-07, 2.7715e+01, 1.4659e-01, \n", " 2DIAGNOSTIC, 143, -5.268845907093e-01, 2.329614552559e-07, 2.7845e+01, 1.2974e-01, \n", " 2DIAGNOSTIC, 144, -5.268952476183e-01, 2.793419526118e-07, 2.7989e+01, 1.4348e-01, \n", " 2DIAGNOSTIC, 145, -5.268995101234e-01, 3.323577442652e-07, 2.8162e+01, 1.7380e-01, \n", " 2DIAGNOSTIC, 146, -5.269003477040e-01, 3.827651831930e-07, 2.8303e+01, 1.4059e-01, \n", " 2DIAGNOSTIC, 147, -5.269002503894e-01, 4.164934421765e-07, 2.8531e+01, 2.2807e-01, \n", " 2DIAGNOSTIC, 148, -5.269000894679e-01, 4.299109593450e-07, 2.8715e+01, 1.8437e-01, \n", " 2DIAGNOSTIC, 149, -5.269001106369e-01, 4.200317035253e-07, 2.8851e+01, 1.3544e-01, \n", " 2DIAGNOSTIC, 150, -5.269002398147e-01, 3.835755115747e-07, 2.9027e+01, 1.7595e-01, \n", " 2DIAGNOSTIC, 151, -5.268997336381e-01, 3.353801845095e-07, 2.9184e+01, 1.5679e-01, \n", " 2DIAGNOSTIC, 152, -5.268997950908e-01, 2.784729325718e-07, 2.9332e+01, 1.4826e-01, \n", " 2DIAGNOSTIC, 153, -5.269003473212e-01, 2.252422537470e-07, 2.9493e+01, 1.6104e-01, \n", " 2DIAGNOSTIC, 154, -5.269003713631e-01, 2.079494960802e-07, 2.9648e+01, 1.5498e-01, \n", " 2DIAGNOSTIC, 155, -5.268989583116e-01, 2.005876128834e-07, 2.9788e+01, 1.3964e-01, \n", " 2DIAGNOSTIC, 156, -5.268995524585e-01, 1.989245962579e-07, 2.9934e+01, 1.4631e-01, \n", " 2DIAGNOSTIC, 157, -5.269007087206e-01, 2.013099358782e-07, 3.0070e+01, 1.3645e-01, \n", " 2DIAGNOSTIC, 158, -5.269071366220e-01, 2.249612813107e-07, 3.0194e+01, 1.2385e-01, \n", " 2DIAGNOSTIC, 159, -5.269506887412e-01, 3.932708032830e-07, 3.0350e+01, 1.5558e-01, \n", " 2DIAGNOSTIC, 160, -5.269498432229e-01, 5.345619579298e-07, 3.0573e+01, 2.2356e-01, \n", " 2DIAGNOSTIC, 161, -5.269456166321e-01, 6.277827155300e-07, 3.0791e+01, 2.1803e-01, \n", " 2DIAGNOSTIC, 162, -5.269454651539e-01, 6.801841931888e-07, 3.0940e+01, 1.4910e-01, \n", " 2DIAGNOSTIC, 163, -5.269463783599e-01, 6.886160735884e-07, 3.1110e+01, 1.6919e-01, \n", " 2DIAGNOSTIC, 164, -5.269455591882e-01, 6.437737561441e-07, 3.1271e+01, 1.6142e-01, \n", " 2DIAGNOSTIC, 165, -5.269453609837e-01, 5.504781466457e-07, 3.1389e+01, 1.1795e-01, \n", " 2DIAGNOSTIC, 166, -5.269457370799e-01, 4.294153050227e-07, 3.1535e+01, 1.4597e-01, \n", " 2DIAGNOSTIC, 167, -5.269465248748e-01, 2.939824167549e-07, 3.1682e+01, 1.4672e-01, \n", " 2DIAGNOSTIC, 168, -5.269460182390e-01, 1.647410326931e-07, 3.1804e+01, 1.2247e-01, \n", " 2DIAGNOSTIC, 169, -5.269462099131e-01, 1.790809379155e-07, 3.1951e+01, 1.4701e-01, \n", " 2DIAGNOSTIC, 170, -5.269457171036e-01, 1.903425305020e-07, 3.2127e+01, 1.7587e-01, \n", " 2DIAGNOSTIC, 171, -5.269468402245e-01, 1.913756443334e-07, 3.2304e+01, 1.7744e-01, \n", " 2DIAGNOSTIC, 172, -5.269468342505e-01, 1.911112313471e-07, 3.2907e+01, 6.0238e-01, \n", " 2DIAGNOSTIC, 173, -5.269468342505e-01, 1.932166157226e-07, 3.3158e+01, 2.5150e-01, \n", " 2DIAGNOSTIC, 174, -5.269468342505e-01, 1.919809519942e-07, 3.3311e+01, 1.5294e-01, \n", " 2DIAGNOSTIC, 175, -5.269468342505e-01, 1.892393706685e-07, 3.3548e+01, 2.3664e-01, \n", " 2DIAGNOSTIC, 176, -5.269468342505e-01, 1.868261872316e-07, 3.3704e+01, 1.5639e-01, \n", " 2DIAGNOSTIC, 177, -5.269468342505e-01, 1.862648119737e-07, 3.3864e+01, 1.5938e-01, \n", " 2DIAGNOSTIC, 178, -5.269468342505e-01, 1.835601107685e-07, 3.4021e+01, 1.5754e-01, \n", " 2DIAGNOSTIC, 179, -5.269468342505e-01, 1.810759088124e-07, 3.4186e+01, 1.6451e-01, \n", " 2DIAGNOSTIC, 180, -5.269468342505e-01, 1.767198465393e-07, 3.4354e+01, 1.6864e-01, \n", " 2DIAGNOSTIC, 181, -5.269468342505e-01, 1.757612092500e-07, 3.4575e+01, 2.2057e-01, \n", " 2DIAGNOSTIC, 182, -5.269468342505e-01, 1.747954021646e-07, 3.4746e+01, 1.7071e-01, \n", " 2DIAGNOSTIC, 183, -5.269468342505e-01, 1.738401512177e-07, 3.4913e+01, 1.6776e-01, \n", " 2DIAGNOSTIC, 184, -5.269468342505e-01, 1.728952843446e-07, 3.5066e+01, 1.5246e-01, \n", " 2DIAGNOSTIC, 185, -5.269468342505e-01, 1.719606331470e-07, 3.5217e+01, 1.5138e-01, \n", " 2DIAGNOSTIC, 186, -5.269468342505e-01, 1.710360328410e-07, 3.5377e+01, 1.5948e-01, \n", " 2DIAGNOSTIC, 187, -5.269468342505e-01, 1.701213221683e-07, 3.5538e+01, 1.6140e-01, \n", " 2DIAGNOSTIC, 188, -5.269468342505e-01, 1.692163433004e-07, 3.5717e+01, 1.7907e-01, \n", " 2DIAGNOSTIC, 189, -5.269468342505e-01, 1.683209417524e-07, 3.5885e+01, 1.6806e-01, \n", " 2DIAGNOSTIC, 190, -5.269468342505e-01, 1.674349662875e-07, 3.6042e+01, 1.5702e-01, \n", " 2DIAGNOSTIC, 191, -5.269468342505e-01, 1.665582688472e-07, 3.6210e+01, 1.6736e-01, \n", " 2DIAGNOSTIC, 192, -5.269468342505e-01, 1.656907044423e-07, 3.6387e+01, 1.7701e-01, \n", " 2DIAGNOSTIC, 193, -5.269468342505e-01, 1.648321310953e-07, 3.6571e+01, 1.8410e-01, \n", " 2DIAGNOSTIC, 194, -5.269468342505e-01, 1.639824097621e-07, 3.6728e+01, 1.5760e-01, \n", " 2DIAGNOSTIC, 195, -5.269468342505e-01, 1.631414042512e-07, 3.6897e+01, 1.6857e-01, \n", " 2DIAGNOSTIC, 196, -5.269468342505e-01, 1.623089811329e-07, 3.7062e+01, 1.6525e-01, \n", " 2DIAGNOSTIC, 197, -5.269468342505e-01, 1.614850097115e-07, 3.7245e+01, 1.8298e-01, \n", " 2DIAGNOSTIC, 198, -5.269468342505e-01, 1.606693619174e-07, 3.7473e+01, 2.2779e-01, \n", " 2DIAGNOSTIC, 199, -5.269468342505e-01, 1.598619122599e-07, 3.7651e+01, 1.7803e-01, \n", " 2DIAGNOSTIC, 200, -5.269468342505e-01, 1.590625377532e-07, 3.7818e+01, 1.6685e-01, \n", " 2DIAGNOSTIC, 201, -5.269468342505e-01, 1.582711178652e-07, 3.8010e+01, 1.9234e-01, \n", " 2DIAGNOSTIC, 202, -5.269468342505e-01, 1.574875344457e-07, 3.8180e+01, 1.7013e-01, \n", " 2DIAGNOSTIC, 203, -5.269468342505e-01, 1.567116716776e-07, 3.8378e+01, 1.9817e-01, \n", " 2DIAGNOSTIC, 204, -5.269468342505e-01, 1.559434160119e-07, 3.8594e+01, 2.1603e-01, \n", " 2DIAGNOSTIC, 205, -5.269468342505e-01, 1.551826561219e-07, 3.8776e+01, 1.8196e-01, \n", " 2DIAGNOSTIC, 206, -5.269468342505e-01, 1.544292828302e-07, 3.8963e+01, 1.8674e-01, \n", " 2DIAGNOSTIC, 207, -5.269468342505e-01, 1.536831890836e-07, 3.9144e+01, 1.8106e-01, \n", " 2DIAGNOSTIC, 208, -5.269468342505e-01, 1.529442698730e-07, 3.9350e+01, 2.0564e-01, \n", " 2DIAGNOSTIC, 209, -5.269468342505e-01, 1.522124222116e-07, 3.9552e+01, 2.0178e-01, \n", " 2DIAGNOSTIC, 210, -5.269468342505e-01, 1.514875450637e-07, 3.9735e+01, 1.8301e-01, \n", " 2DIAGNOSTIC, 211, -5.269468342505e-01, 1.507695393220e-07, 3.9896e+01, 1.6096e-01, \n", " 2DIAGNOSTIC, 212, -5.269468342505e-01, 1.500583077354e-07, 4.0050e+01, 1.5462e-01, \n", " 2DIAGNOSTIC, 213, -5.269468342505e-01, 1.493537548896e-07, 4.0221e+01, 1.7112e-01, \n", " 2DIAGNOSTIC, 214, -5.269468342505e-01, 1.486557871487e-07, 4.0441e+01, 2.1935e-01, \n", " 2DIAGNOSTIC, 215, -5.269468342505e-01, 1.479643126209e-07, 4.0601e+01, 1.6020e-01, \n", " 2DIAGNOSTIC, 216, -5.269468342505e-01, 1.472792411188e-07, 4.0779e+01, 1.7808e-01, \n", " 2DIAGNOSTIC, 217, -5.269468342505e-01, 1.466004841124e-07, 4.0964e+01, 1.8490e-01, \n", " 2DIAGNOSTIC, 218, -5.269468342505e-01, 1.459279547001e-07, 4.1142e+01, 1.7772e-01, \n", " 2DIAGNOSTIC, 219, -5.269468342505e-01, 1.452615675610e-07, 4.1321e+01, 1.7895e-01, \n", " 2DIAGNOSTIC, 220, -5.269468342505e-01, 1.446012389350e-07, 4.1493e+01, 1.7214e-01, \n", " 2DIAGNOSTIC, 221, -5.269468342505e-01, 1.439468865737e-07, 4.1667e+01, 1.7422e-01, \n", " 2DIAGNOSTIC, 222, -5.269468342505e-01, 1.432984297143e-07, 4.1836e+01, 1.6933e-01, \n", " 2DIAGNOSTIC, 223, -5.269468342505e-01, 1.426557890288e-07, 4.2017e+01, 1.8086e-01, \n", " 2DIAGNOSTIC, 224, -5.269468342505e-01, 1.420188866282e-07, 4.2202e+01, 1.8490e-01, \n", " 2DIAGNOSTIC, 225, -5.269468342505e-01, 1.413876459903e-07, 4.2397e+01, 1.9452e-01, \n", " 2DIAGNOSTIC, 226, -5.269468342505e-01, 1.407619919557e-07, 4.2575e+01, 1.7852e-01, \n", " 2DIAGNOSTIC, 227, -5.269468342505e-01, 1.401418506840e-07, 4.2748e+01, 1.7335e-01, \n", " 2DIAGNOSTIC, 228, -5.269468342505e-01, 1.395271496344e-07, 4.2937e+01, 1.8812e-01, \n", " 2DIAGNOSTIC, 229, -5.269468342505e-01, 1.389178175349e-07, 4.3120e+01, 1.8394e-01, \n", " 2DIAGNOSTIC, 230, -5.269468342505e-01, 1.383137843512e-07, 4.3303e+01, 1.8206e-01, \n", " 2DIAGNOSTIC, 231, -5.269468342505e-01, 1.377149812572e-07, 4.3479e+01, 1.7607e-01, \n", " 2DIAGNOSTIC, 232, -5.269468342505e-01, 1.371213406215e-07, 4.3644e+01, 1.6553e-01, \n", " 2DIAGNOSTIC, 233, -5.269468342505e-01, 1.365327959701e-07, 4.3824e+01, 1.7939e-01, \n", " 2DIAGNOSTIC, 234, -5.269468342505e-01, 1.359492819630e-07, 4.3994e+01, 1.7003e-01, \n", " 2DIAGNOSTIC, 235, -5.269468342505e-01, 1.353707343782e-07, 4.4166e+01, 1.7198e-01, \n", " 2DIAGNOSTIC, 236, -5.269468342505e-01, 1.347970900751e-07, 4.4312e+01, 1.4611e-01, \n", " 2DIAGNOSTIC, 237, -5.269468342505e-01, 1.342282869845e-07, 4.4480e+01, 1.6811e-01, \n", " 2DIAGNOSTIC, 238, -5.269468342505e-01, 1.336642640772e-07, 4.4637e+01, 1.5766e-01, \n", " 2DIAGNOSTIC, 239, -5.269468342505e-01, 1.331049613480e-07, 4.4799e+01, 1.6114e-01, \n", " 2DIAGNOSTIC, 240, -5.269468342505e-01, 1.325503197905e-07, 4.4965e+01, 1.6634e-01, \n", " 2DIAGNOSTIC, 241, -5.269468342505e-01, 1.320002813773e-07, 4.5113e+01, 1.4773e-01, \n", " 2DIAGNOSTIC, 242, -5.269468342505e-01, 1.314547890411e-07, 4.5303e+01, 1.9000e-01, \n", " 2DIAGNOSTIC, 243, -5.269468342505e-01, 1.309137866558e-07, 4.5477e+01, 1.7421e-01, \n", " 2DIAGNOSTIC, 244, -5.269468342505e-01, 1.303772190105e-07, 4.5642e+01, 1.6561e-01, \n", " 2DIAGNOSTIC, 245, -5.269468342505e-01, 1.298450317986e-07, 4.5818e+01, 1.7584e-01, \n", " 2DIAGNOSTIC, 246, -5.269468342505e-01, 1.293171716004e-07, 4.5998e+01, 1.7965e-01, \n", " 2DIAGNOSTIC, 247, -5.269468342505e-01, 1.287935858518e-07, 4.6185e+01, 1.8727e-01, \n", " 2DIAGNOSTIC, 248, -5.269468342505e-01, 1.282742228513e-07, 4.6353e+01, 1.6802e-01, \n", " 2DIAGNOSTIC, 249, -5.269468342505e-01, 1.277590317081e-07, 4.6531e+01, 1.7742e-01, \n", " 2DIAGNOSTIC, 250, -5.269468342505e-01, 1.272479623633e-07, 4.6707e+01, 1.7609e-01, \n", "DIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST\n", " 2DIAGNOSTIC, 1, -4.588735688178e-01, 1.797693134862e+308, 5.1291e+01, 4.5840e+00, \n", " 2DIAGNOSTIC, 2, -4.589790427910e-01, 1.797693134862e+308, 5.2088e+01, 7.9706e-01, \n", " 2DIAGNOSTIC, 3, -4.590936101797e-01, 1.797693134862e+308, 5.2849e+01, 7.6133e-01, \n", " 2DIAGNOSTIC, 4, -4.591816120425e-01, 1.797693134862e+308, 5.3729e+01, 8.7957e-01, \n", " 2DIAGNOSTIC, 5, -4.591827583614e-01, 1.797693134862e+308, 5.5029e+01, 1.3006e+00, \n", " 2DIAGNOSTIC, 6, -4.591827414129e-01, 1.797693134862e+308, 5.5816e+01, 7.8668e-01, \n", " 2DIAGNOSTIC, 7, -4.591821919089e-01, 1.797693134862e+308, 5.6997e+01, 1.1813e+00, \n", " 2DIAGNOSTIC, 8, -4.591825051190e-01, 1.797693134862e+308, 5.7872e+01, 8.7500e-01, \n", " 2DIAGNOSTIC, 9, -4.591815534538e-01, 1.797693134862e+308, 5.8784e+01, 9.1128e-01, \n", " 2DIAGNOSTIC, 10, -4.591814538241e-01, 3.707196803528e-05, 5.9845e+01, 1.0610e+00, \n", " 2DIAGNOSTIC, 11, -4.591814065862e-01, 1.858413319049e-05, 6.0819e+01, 9.7466e-01, \n", " 2DIAGNOSTIC, 12, -4.591813357390e-01, 7.093970513239e-06, 6.1687e+01, 8.6766e-01, \n", " 2DIAGNOSTIC, 13, -4.591813118928e-01, 2.305167835434e-06, 6.2722e+01, 1.0352e+00, \n", " 2DIAGNOSTIC, 14, -4.591810363931e-01, 2.091019669470e-06, 6.3601e+01, 8.7880e-01, \n", " 2DIAGNOSTIC, 15, -4.591809939299e-01, 1.967981234113e-06, 6.4337e+01, 7.3581e-01, \n", " 2DIAGNOSTIC, 16, -4.591809477024e-01, 1.872011952772e-06, 6.5092e+01, 7.5564e-01, \n", " 2DIAGNOSTIC, 17, -4.591808886859e-01, 1.774995764828e-06, 6.5957e+01, 8.6413e-01, \n", " 2DIAGNOSTIC, 18, -4.591809634217e-01, 1.711943126245e-06, 6.6740e+01, 7.8388e-01, \n", " 2DIAGNOSTIC, 19, -4.591809514471e-01, 1.629346894474e-06, 6.7605e+01, 8.6469e-01, \n", " 2DIAGNOSTIC, 20, -4.591809345962e-01, 1.555656582830e-06, 6.8352e+01, 7.4696e-01, \n", " 2DIAGNOSTIC, 21, -4.591811166159e-01, 1.496211432403e-06, 6.9168e+01, 8.1631e-01, \n", " 2DIAGNOSTIC, 22, -4.591812009792e-01, 1.444064802389e-06, 7.0139e+01, 9.7064e-01, \n", " 2DIAGNOSTIC, 23, -4.591813609701e-01, 1.400435344835e-06, 7.0998e+01, 8.5903e-01, \n", " 2DIAGNOSTIC, 24, -4.591812598174e-01, 1.349080933931e-06, 7.1833e+01, 8.3530e-01, \n", " 2DIAGNOSTIC, 25, -4.591813367260e-01, 1.300662034666e-06, 7.2952e+01, 1.1185e+00, \n", " 2DIAGNOSTIC, 26, -4.591813074587e-01, 1.251477048131e-06, 7.3985e+01, 1.0329e+00, \n", " 2DIAGNOSTIC, 27, -4.591812197912e-01, 1.199821264695e-06, 7.4817e+01, 8.3265e-01, \n", " 2DIAGNOSTIC, 28, -4.591811862426e-01, 1.150812534496e-06, 7.5873e+01, 1.0557e+00, \n", " 2DIAGNOSTIC, 29, -4.591811407150e-01, 1.102660760290e-06, 7.6734e+01, 8.6098e-01, \n", " 2DIAGNOSTIC, 30, -4.591810998208e-01, 1.055926703630e-06, 7.7555e+01, 8.2105e-01, \n", " 2DIAGNOSTIC, 31, -4.591810496926e-01, 1.015232011001e-06, 7.8350e+01, 7.9463e-01, \n", " 2DIAGNOSTIC, 32, -4.591810150335e-01, 9.790276017940e-07, 7.9253e+01, 9.0342e-01, \n", " 2DIAGNOSTIC, 33, -4.591809885333e-01, 9.490286209599e-07, 8.0282e+01, 1.0289e+00, \n", " 2DIAGNOSTIC, 34, -4.591809502511e-01, 9.196126674049e-07, 8.1109e+01, 8.2684e-01, \n", " 2DIAGNOSTIC, 35, -4.591807502729e-01, 8.912312556772e-07, 8.1841e+01, 7.3259e-01, \n", " 2DIAGNOSTIC, 36, -4.591807126189e-01, 8.650810624684e-07, 8.2719e+01, 8.7723e-01, \n", " 2DIAGNOSTIC, 37, -4.591807556634e-01, 8.413418283171e-07, 8.3661e+01, 9.4213e-01, \n", " 2DIAGNOSTIC, 38, -4.591806860474e-01, 8.188567145358e-07, 8.4571e+01, 9.1005e-01, \n", " 2DIAGNOSTIC, 39, -4.591808450692e-01, 8.011214570822e-07, 8.5565e+01, 9.9386e-01, \n", " 2DIAGNOSTIC, 40, -4.591808166781e-01, 7.845811362192e-07, 8.6460e+01, 8.9483e-01, \n", " 2DIAGNOSTIC, 41, -4.591807877695e-01, 7.687181197667e-07, 8.7380e+01, 9.2012e-01, \n", " 2DIAGNOSTIC, 42, -4.591807515130e-01, 7.532457922781e-07, 8.8319e+01, 9.3962e-01, \n", " 2DIAGNOSTIC, 43, -4.591796984679e-01, 7.233326753502e-07, 8.9307e+01, 9.8731e-01, \n", " 2DIAGNOSTIC, 44, -4.591796692702e-01, 6.958653816259e-07, 9.0148e+01, 8.4121e-01, \n", " 2DIAGNOSTIC, 45, -4.591795275194e-01, 6.673462421003e-07, 9.1123e+01, 9.7475e-01, \n", " 2DIAGNOSTIC, 46, -4.591795880701e-01, 6.439962282785e-07, 9.2276e+01, 1.1535e+00, \n", " 2DIAGNOSTIC, 47, -4.591795076239e-01, 6.257542931667e-07, 9.3145e+01, 8.6927e-01, \n", " 2DIAGNOSTIC, 48, -4.591794072705e-01, 6.111441369951e-07, 9.4065e+01, 9.1967e-01, \n", " 2DIAGNOSTIC, 49, -4.591793658699e-01, 6.036562077531e-07, 9.4846e+01, 7.8139e-01, \n", " 2DIAGNOSTIC, 50, -4.591793773529e-01, 6.004277997157e-07, 9.5628e+01, 7.8207e-01, \n", " 2DIAGNOSTIC, 51, -4.591793489434e-01, 5.998826559696e-07, 9.6515e+01, 8.8655e-01, \n", " 2DIAGNOSTIC, 52, -4.591793237147e-01, 6.012641554018e-07, 9.7254e+01, 7.3911e-01, \n", " 2DIAGNOSTIC, 53, -4.591793428940e-01, 5.915580875183e-07, 9.8083e+01, 8.2915e-01, \n", " 2DIAGNOSTIC, 54, -4.591793514378e-01, 5.828411039702e-07, 9.8824e+01, 7.4072e-01, \n", " 2DIAGNOSTIC, 55, -4.591793878826e-01, 5.738027372380e-07, 1.0002e+02, 1.1956e+00, \n", " 2DIAGNOSTIC, 56, -4.591793991842e-01, 5.663241199293e-07, 1.0087e+02, 8.5192e-01, \n", " 2DIAGNOSTIC, 57, -4.591793620794e-01, 5.580325256258e-07, 1.0170e+02, 8.2531e-01, \n", " 2DIAGNOSTIC, 58, -4.591792764126e-01, 5.480718114140e-07, 1.0244e+02, 7.3937e-01, \n", " 2DIAGNOSTIC, 59, -4.591791300328e-01, 5.365237956238e-07, 1.0318e+02, 7.3948e-01, \n", " 2DIAGNOSTIC, 60, -4.591791315003e-01, 5.257757010498e-07, 1.0389e+02, 7.1171e-01, \n", " 2DIAGNOSTIC, 61, -4.591793334431e-01, 5.175407485347e-07, 1.0473e+02, 8.4197e-01, \n", " 2DIAGNOSTIC, 62, -4.591795969443e-01, 5.122587506193e-07, 1.0556e+02, 8.3528e-01, \n", " 2DIAGNOSTIC, 63, -4.591784420568e-01, 4.960399578452e-07, 1.0651e+02, 9.4058e-01, \n", " 2DIAGNOSTIC, 64, -4.591783830963e-01, 4.810904653124e-07, 1.0739e+02, 8.7983e-01, \n", " 2DIAGNOSTIC, 65, -4.591784244851e-01, 4.687796598159e-07, 1.0826e+02, 8.7958e-01, \n", " 2DIAGNOSTIC, 66, -4.591783524575e-01, 4.580003222371e-07, 1.0916e+02, 8.9091e-01, \n", " 2DIAGNOSTIC, 67, -4.591783265636e-01, 4.492844479960e-07, 1.0988e+02, 7.2760e-01, \n", " 2DIAGNOSTIC, 68, -4.591783731518e-01, 4.431701905137e-07, 1.1066e+02, 7.7297e-01, \n", " 2DIAGNOSTIC, 69, -4.591784647617e-01, 4.391972698026e-07, 1.1154e+02, 8.8780e-01, \n", " 2DIAGNOSTIC, 70, -4.591786129324e-01, 4.385516313692e-07, 1.1230e+02, 7.5985e-01, \n", " 2DIAGNOSTIC, 71, -4.591787523130e-01, 4.422250846556e-07, 1.1317e+02, 8.6456e-01, \n", " 2DIAGNOSTIC, 72, -4.591787215432e-01, 4.486404249146e-07, 1.1427e+02, 1.1003e+00, \n", " 2DIAGNOSTIC, 73, -4.591786451855e-01, 4.438235009577e-07, 1.1513e+02, 8.6471e-01, \n", " 2DIAGNOSTIC, 74, -4.591785116060e-01, 4.367425109203e-07, 1.1603e+02, 8.9917e-01, \n", " 2DIAGNOSTIC, 75, -4.591784953071e-01, 4.294068679540e-07, 1.1690e+02, 8.6547e-01, \n", " 2DIAGNOSTIC, 76, -4.591784175091e-01, 4.205161113578e-07, 1.1777e+02, 8.6809e-01, \n", " 2DIAGNOSTIC, 77, -4.591783342174e-01, 4.108081469775e-07, 1.1847e+02, 7.0079e-01, \n", " 2DIAGNOSTIC, 78, -4.591783209655e-01, 4.018728621547e-07, 1.1930e+02, 8.2979e-01, \n", " 2DIAGNOSTIC, 79, -4.591784817199e-01, 3.956973063327e-07, 1.2000e+02, 7.0483e-01, \n", " 2DIAGNOSTIC, 80, -4.591784972376e-01, 3.915329077325e-07, 1.2103e+02, 1.0284e+00, \n", " 2DIAGNOSTIC, 81, -4.591785259869e-01, 3.893507258615e-07, 1.2191e+02, 8.8494e-01, \n", " 2DIAGNOSTIC, 82, -4.591784329559e-01, 3.866433948407e-07, 1.2275e+02, 8.3432e-01, \n", " 2DIAGNOSTIC, 83, -4.591783380779e-01, 3.828901946751e-07, 1.2349e+02, 7.4420e-01, \n", " 2DIAGNOSTIC, 84, -4.591783582060e-01, 3.784074673972e-07, 1.2432e+02, 8.2302e-01, \n", " 2DIAGNOSTIC, 85, -4.591784330304e-01, 3.744607813948e-07, 1.2508e+02, 7.6853e-01, \n", " 2DIAGNOSTIC, 86, -4.591785122305e-01, 3.706032259149e-07, 1.2596e+02, 8.7817e-01, \n", " 2DIAGNOSTIC, 87, -4.591784939262e-01, 3.660661767133e-07, 1.2673e+02, 7.6322e-01, \n", " 2DIAGNOSTIC, 88, -4.591783938024e-01, 3.607975187364e-07, 1.2772e+02, 9.9223e-01, \n", " 2DIAGNOSTIC, 89, -4.591784146742e-01, 3.569907312487e-07, 1.2853e+02, 8.1552e-01, \n", " 2DIAGNOSTIC, 90, -4.591783912354e-01, 3.532057560162e-07, 1.2942e+02, 8.8492e-01, \n", " 2DIAGNOSTIC, 91, -4.591783698508e-01, 3.495746934579e-07, 1.3014e+02, 7.2290e-01, \n", " 2DIAGNOSTIC, 92, -4.591783517357e-01, 3.453089748359e-07, 1.3100e+02, 8.5830e-01, \n", " 2DIAGNOSTIC, 93, -4.591783259633e-01, 3.403971418348e-07, 1.3178e+02, 7.8063e-01, \n", " 2DIAGNOSTIC, 94, -4.591782922280e-01, 3.356518329632e-07, 1.3252e+02, 7.3856e-01, \n", " 2DIAGNOSTIC, 95, -4.591782588938e-01, 3.315214676721e-07, 1.3328e+02, 7.6296e-01, \n", " 2DIAGNOSTIC, 96, -4.591783545298e-01, 3.289280096960e-07, 1.3421e+02, 9.3252e-01, \n", " 2DIAGNOSTIC, 97, -4.591783534076e-01, 3.264962335162e-07, 1.3527e+02, 1.0597e+00, \n", " 2DIAGNOSTIC, 98, -4.591783723811e-01, 3.237416419492e-07, 1.3618e+02, 9.0562e-01, \n", " 2DIAGNOSTIC, 99, -4.591783342147e-01, 3.210291038124e-07, 1.3708e+02, 8.9829e-01, \n", " 2DIAGNOSTIC, 100, -4.591782428653e-01, 3.176980194145e-07, 1.3785e+02, 7.7277e-01, \n", " Elapsed time (stage 0): 1.3958e+02\n", "\n", "\n", "Stage 1\n", " iterations = 1000x500x250x100\n", " convergence threshold = 1.0000e-08\n", " convergence window size = 10\n", " number of levels = 4\n", " using the Mattes MI metric (number of bins = 32, weight = 1.0000e+00)\n", " preprocessing: winsorizing the image intensities\n", " preprocessing: histogram matching the images\n", " Shrink factors (level 1 out of 4): [8, 8, 8]\n", " Shrink factors (level 2 out of 4): [4, 4, 4]\n", " Shrink factors (level 3 out of 4): [2, 2, 2]\n", " Shrink factors (level 4 out of 4): [1, 1, 1]\n", " smoothing sigmas per level: [4, 2, 1, 0]\n", " regular sampling (percentage = 2.5000e-01)\n", "\n", "*** Running AffineTransform registration ***\n", "\n", "DIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST\n", " 2DIAGNOSTIC, 1, -7.624100392495e-01, 1.797693134862e+308, 1.3259e+00, 1.3259e+00, \n", " 2DIAGNOSTIC, 2, -7.627435550185e-01, 1.797693134862e+308, 1.3298e+00, 3.8462e-03, \n", " 2DIAGNOSTIC, 3, -7.632071602644e-01, 1.797693134862e+308, 1.3362e+00, 6.4831e-03, \n", " 2DIAGNOSTIC, 4, -7.632851454641e-01, 1.797693134862e+308, 1.3409e+00, 4.6721e-03, \n", " 2DIAGNOSTIC, 5, -7.633057053139e-01, 1.797693134862e+308, 1.3447e+00, 3.7990e-03, \n", " 2DIAGNOSTIC, 6, -7.632288137625e-01, 1.797693134862e+308, 1.3486e+00, 3.8691e-03, \n", " 2DIAGNOSTIC, 7, -7.635091021585e-01, 1.797693134862e+308, 1.3530e+00, 4.4270e-03, \n", " 2DIAGNOSTIC, 8, -7.637569002535e-01, 1.797693134862e+308, 1.3575e+00, 4.5102e-03, \n", " 2DIAGNOSTIC, 9, -7.638835274629e-01, 1.797693134862e+308, 1.3613e+00, 3.7451e-03, \n", " 2DIAGNOSTIC, 10, -7.640655586382e-01, 1.196887294747e-04, 1.3667e+00, 5.4879e-03, \n", " 2DIAGNOSTIC, 11, -7.641865948439e-01, 1.000257894395e-04, 1.3723e+00, 5.5342e-03, \n", " 2DIAGNOSTIC, 12, -7.642217909365e-01, 8.585726067804e-05, 1.3771e+00, 4.8609e-03, \n", " 2DIAGNOSTIC, 13, -7.643365741862e-01, 8.275976155400e-05, 1.3846e+00, 7.5059e-03, \n", " 2DIAGNOSTIC, 14, -7.643598175472e-01, 7.546012899287e-05, 1.3902e+00, 5.5730e-03, \n", " 2DIAGNOSTIC, 15, -7.640754786457e-01, 5.608224647145e-05, 1.3957e+00, 5.5110e-03, \n", " 2DIAGNOSTIC, 16, -7.640744277464e-01, 3.247011343234e-05, 1.4005e+00, 4.7851e-03, \n", " 2DIAGNOSTIC, 17, -7.641119657883e-01, 1.563326727660e-05, 1.4053e+00, 4.8029e-03, \n", " 2DIAGNOSTIC, 18, -7.642830361803e-01, 7.904880942933e-06, 1.4108e+00, 5.4810e-03, \n", " 2DIAGNOSTIC, 19, -7.643882912844e-01, 4.818461805021e-06, 1.4164e+00, 5.5768e-03, \n", " 2DIAGNOSTIC, 20, -7.644624634929e-01, 6.575018113603e-06, 1.4211e+00, 4.7140e-03, \n", " 2DIAGNOSTIC, 21, -7.645635046376e-01, 1.169903894709e-05, 1.4265e+00, 5.4529e-03, \n", " 2DIAGNOSTIC, 22, -7.644430179084e-01, 1.380814659976e-05, 1.4320e+00, 5.4629e-03, \n", " 2DIAGNOSTIC, 23, -7.644732051997e-01, 1.689537577184e-05, 1.4381e+00, 6.0511e-03, \n", " 2DIAGNOSTIC, 24, -7.643909749492e-01, 1.744043852087e-05, 1.4435e+00, 5.4312e-03, \n", " 2DIAGNOSTIC, 25, -7.645090475695e-01, 1.398400466542e-05, 1.4483e+00, 4.8029e-03, \n", " 2DIAGNOSTIC, 26, -7.639208394361e-01, 1.128423214557e-06, 1.4536e+00, 5.2948e-03, \n", "DIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST\n", " 2DIAGNOSTIC, 1, -6.058926197619e-01, 1.797693134862e+308, 2.6771e+00, 1.2235e+00, \n", " 2DIAGNOSTIC, 2, -6.063493341076e-01, 1.797693134862e+308, 2.6990e+00, 2.1836e-02, \n", " 2DIAGNOSTIC, 3, -6.069941825434e-01, 1.797693134862e+308, 2.7213e+00, 2.2372e-02, \n", " 2DIAGNOSTIC, 4, -6.080468387714e-01, 1.797693134862e+308, 2.7485e+00, 2.7144e-02, \n", " 2DIAGNOSTIC, 5, -6.094572836768e-01, 1.797693134862e+308, 2.7732e+00, 2.4735e-02, \n", " 2DIAGNOSTIC, 6, -6.114505255395e-01, 1.797693134862e+308, 2.7963e+00, 2.3110e-02, \n", " 2DIAGNOSTIC, 7, -6.167519756028e-01, 1.797693134862e+308, 2.8243e+00, 2.7943e-02, \n", " 2DIAGNOSTIC, 8, -6.179938546441e-01, 1.797693134862e+308, 2.8707e+00, 4.6482e-02, \n", " 2DIAGNOSTIC, 9, -6.180158636895e-01, 1.797693134862e+308, 2.8920e+00, 2.1304e-02, \n", " 2DIAGNOSTIC, 10, -6.180121986274e-01, 1.602264281727e-03, 2.9201e+00, 2.8059e-02, \n", " 2DIAGNOSTIC, 11, -6.180203527746e-01, 1.401682547545e-03, 2.9426e+00, 2.2515e-02, \n", " 2DIAGNOSTIC, 12, -6.180132972886e-01, 1.123605098767e-03, 2.9646e+00, 2.1985e-02, \n", " 2DIAGNOSTIC, 13, -6.180122059622e-01, 8.096768017885e-04, 2.9891e+00, 2.4469e-02, \n", " 2DIAGNOSTIC, 14, -6.180120926542e-01, 5.046113947327e-04, 3.0123e+00, 2.3260e-02, \n", " 2DIAGNOSTIC, 15, -6.180097922229e-01, 2.389407252082e-04, 3.0317e+00, 1.9384e-02, \n", " 2DIAGNOSTIC, 16, -6.180100551964e-01, 3.867815114492e-05, 3.0521e+00, 2.0388e-02, \n", " 2DIAGNOSTIC, 17, -6.180208532297e-01, 2.322904659638e-06, 3.0747e+00, 2.2614e-02, \n", " 2DIAGNOSTIC, 18, -6.180314414862e-01, 2.143079375135e-06, 3.0977e+00, 2.3034e-02, \n", " 2DIAGNOSTIC, 19, -6.180313166944e-01, 2.479238927988e-06, 3.1205e+00, 2.2742e-02, \n", " 2DIAGNOSTIC, 20, -6.180457540078e-01, 2.956750911297e-06, 3.1404e+00, 1.9902e-02, \n", " 2DIAGNOSTIC, 21, -6.180729996955e-01, 4.038911822914e-06, 3.1632e+00, 2.2817e-02, \n", " 2DIAGNOSTIC, 22, -6.180871745557e-01, 4.919171899216e-06, 3.1877e+00, 2.4462e-02, \n", " 2DIAGNOSTIC, 23, -6.180795275216e-01, 5.221183063467e-06, 3.2094e+00, 2.1715e-02, \n", " 2DIAGNOSTIC, 24, -6.180919933441e-01, 5.395407430414e-06, 3.2310e+00, 2.1660e-02, \n", " 2DIAGNOSTIC, 25, -6.181042823473e-01, 5.353550987762e-06, 3.2543e+00, 2.3287e-02, \n", " 2DIAGNOSTIC, 26, -6.181291935944e-01, 5.359436264632e-06, 3.2768e+00, 2.2434e-02, \n", " 2DIAGNOSTIC, 27, -6.181404688071e-01, 5.340425301752e-06, 3.2990e+00, 2.2256e-02, \n", " 2DIAGNOSTIC, 28, -6.181405640846e-01, 5.120401191952e-06, 3.3231e+00, 2.4061e-02, \n", " 2DIAGNOSTIC, 29, -6.180692145460e-01, 3.409843316864e-06, 3.3460e+00, 2.2866e-02, \n", " 2DIAGNOSTIC, 30, -6.180771624748e-01, 1.957220977060e-06, 3.3730e+00, 2.7051e-02, \n", " 2DIAGNOSTIC, 31, -6.180578871938e-01, 6.045810301211e-07, 3.3982e+00, 2.5164e-02, \n", "DIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST\n", " 2DIAGNOSTIC, 1, -5.359358630919e-01, 1.797693134862e+308, 4.4459e+00, 1.0478e+00, \n", " 2DIAGNOSTIC, 2, -5.361639283112e-01, 1.797693134862e+308, 4.6054e+00, 1.5950e-01, \n", " 2DIAGNOSTIC, 3, -5.363450052039e-01, 1.797693134862e+308, 4.7813e+00, 1.7584e-01, \n", " 2DIAGNOSTIC, 4, -5.365138761180e-01, 1.797693134862e+308, 4.9350e+00, 1.5376e-01, \n", " 2DIAGNOSTIC, 5, -5.367406164644e-01, 1.797693134862e+308, 5.1022e+00, 1.6716e-01, \n", " 2DIAGNOSTIC, 6, -5.369618229440e-01, 1.797693134862e+308, 5.3030e+00, 2.0080e-01, \n", " 2DIAGNOSTIC, 7, -5.369684435822e-01, 1.797693134862e+308, 5.5563e+00, 2.5334e-01, \n", " 2DIAGNOSTIC, 8, -5.370386627275e-01, 1.797693134862e+308, 5.7345e+00, 1.7819e-01, \n", " 2DIAGNOSTIC, 9, -5.371792701049e-01, 1.797693134862e+308, 5.9189e+00, 1.8436e-01, \n", " 2DIAGNOSTIC, 10, -5.374068547389e-01, 1.670045985112e-04, 6.0753e+00, 1.5642e-01, \n", " 2DIAGNOSTIC, 11, -5.376582844405e-01, 1.487003878774e-04, 6.2690e+00, 1.9370e-01, \n", " 2DIAGNOSTIC, 12, -5.376550005146e-01, 1.301711221697e-04, 6.5870e+00, 3.1800e-01, \n", " 2DIAGNOSTIC, 13, -5.376548051282e-01, 1.106171929478e-04, 6.7697e+00, 1.8267e-01, \n", " 2DIAGNOSTIC, 14, -5.376541174147e-01, 9.027519064339e-05, 6.9477e+00, 1.7808e-01, \n", " 2DIAGNOSTIC, 15, -5.376531421698e-01, 7.221126635483e-05, 7.1291e+00, 1.8135e-01, \n", " 2DIAGNOSTIC, 16, -5.376533716711e-01, 5.723476953488e-05, 7.2877e+00, 1.5857e-01, \n", " 2DIAGNOSTIC, 17, -5.376531282236e-01, 3.921196860446e-05, 7.4862e+00, 1.9849e-01, \n", " 2DIAGNOSTIC, 18, -5.376535862724e-01, 2.190503509188e-05, 7.6519e+00, 1.6578e-01, \n", " 2DIAGNOSTIC, 19, -5.376525537170e-01, 8.343695445862e-06, 7.8047e+00, 1.5278e-01, \n", " 2DIAGNOSTIC, 20, -5.376524349844e-01, 1.346739623605e-06, 7.9908e+00, 1.8605e-01, \n", " 2DIAGNOSTIC, 21, -5.376537086267e-01, 1.407838152265e-06, 8.1537e+00, 1.6291e-01, \n", " 2DIAGNOSTIC, 22, -5.376449831921e-01, 1.182975447850e-06, 8.3412e+00, 1.8757e-01, \n", " 2DIAGNOSTIC, 23, -5.376442821152e-01, 9.880164012627e-07, 8.5997e+00, 2.5850e-01, \n", " 2DIAGNOSTIC, 24, -5.376433079102e-01, 8.093384665023e-07, 8.7604e+00, 1.6065e-01, \n", " 2DIAGNOSTIC, 25, -5.376429651931e-01, 6.630064373001e-07, 8.9381e+00, 1.7766e-01, \n", " 2DIAGNOSTIC, 26, -5.376416075570e-01, 5.622630180821e-07, 9.1376e+00, 1.9950e-01, \n", " 2DIAGNOSTIC, 27, -5.376420166135e-01, 5.372535156339e-07, 9.3746e+00, 2.3702e-01, \n", " 2DIAGNOSTIC, 28, -5.376408810124e-01, 5.629529542736e-07, 9.5454e+00, 1.7080e-01, \n", " 2DIAGNOSTIC, 29, -5.376403724255e-01, 6.113563960283e-07, 9.7185e+00, 1.7318e-01, \n", " 2DIAGNOSTIC, 30, -5.376399118956e-01, 6.899765135140e-07, 9.9074e+00, 1.8883e-01, \n", " 2DIAGNOSTIC, 31, -5.376381843724e-01, 7.949370970789e-07, 1.0075e+01, 1.6718e-01, \n", " 2DIAGNOSTIC, 32, -5.376370764940e-01, 7.534420344915e-07, 1.0219e+01, 1.4478e-01, \n", " 2DIAGNOSTIC, 33, -5.376373750533e-01, 7.312768129306e-07, 1.0369e+01, 1.4917e-01, \n", " 2DIAGNOSTIC, 34, -5.376377257204e-01, 7.223009252308e-07, 1.0509e+01, 1.4071e-01, \n", " 2DIAGNOSTIC, 35, -5.376376826150e-01, 7.285752041432e-07, 1.0685e+01, 1.7546e-01, \n", " 2DIAGNOSTIC, 36, -5.376374493953e-01, 7.284857816044e-07, 1.0865e+01, 1.8014e-01, \n", " 2DIAGNOSTIC, 37, -5.376372192018e-01, 7.465437029189e-07, 1.1032e+01, 1.6705e-01, \n", " 2DIAGNOSTIC, 38, -5.376325772037e-01, 6.938070368674e-07, 1.1218e+01, 1.8596e-01, \n", " 2DIAGNOSTIC, 39, -5.376320669796e-01, 6.449215922341e-07, 1.1357e+01, 1.3939e-01, \n", " 2DIAGNOSTIC, 40, -5.376314020554e-01, 5.998664015308e-07, 1.1530e+01, 1.7281e-01, \n", " 2DIAGNOSTIC, 41, -5.376313572110e-01, 5.526088003860e-07, 1.1696e+01, 1.6596e-01, \n", " 2DIAGNOSTIC, 42, -5.376311948332e-01, 5.129812582355e-07, 1.1875e+01, 1.7859e-01, \n", " 2DIAGNOSTIC, 43, -5.376311302393e-01, 5.021898065762e-07, 1.2034e+01, 1.5925e-01, \n", " 2DIAGNOSTIC, 44, -5.376308613632e-01, 5.158781251867e-07, 1.2258e+01, 2.2393e-01, \n", " 2DIAGNOSTIC, 45, -5.376324755870e-01, 5.666129434152e-07, 1.2453e+01, 1.9573e-01, \n", " 2DIAGNOSTIC, 46, -5.376206083989e-01, 4.882879952560e-07, 1.2646e+01, 1.9289e-01, \n", " 2DIAGNOSTIC, 47, -5.376201540568e-01, 4.304039805496e-07, 1.2868e+01, 2.2141e-01, \n", " 2DIAGNOSTIC, 48, -5.376189882348e-01, 3.335229851950e-07, 1.3070e+01, 2.0212e-01, \n", " 2DIAGNOSTIC, 49, -5.376190303614e-01, 2.654785278451e-07, 1.3232e+01, 1.6162e-01, \n", " 2DIAGNOSTIC, 50, -5.376185271864e-01, 2.245413448614e-07, 1.3388e+01, 1.5624e-01, \n", " 2DIAGNOSTIC, 51, -5.376180411306e-01, 2.211824814170e-07, 1.3585e+01, 1.9759e-01, \n", " 2DIAGNOSTIC, 52, -5.376174786989e-01, 2.501340175300e-07, 1.3748e+01, 1.6278e-01, \n", " 2DIAGNOSTIC, 53, -5.376170386769e-01, 3.062488863476e-07, 1.3931e+01, 1.8327e-01, \n", " 2DIAGNOSTIC, 54, -5.376180385783e-01, 3.937849352119e-07, 1.4123e+01, 1.9146e-01, \n", " 2DIAGNOSTIC, 55, -5.376164766923e-01, 5.001317561967e-07, 1.4289e+01, 1.6606e-01, \n", " 2DIAGNOSTIC, 56, -5.376174974832e-01, 5.083704486333e-07, 1.4463e+01, 1.7453e-01, \n", " 2DIAGNOSTIC, 57, -5.376169097388e-01, 5.124659804602e-07, 1.4639e+01, 1.7575e-01, \n", " 2DIAGNOSTIC, 58, -5.376171382926e-01, 5.122200587848e-07, 1.4797e+01, 1.5815e-01, \n", " 2DIAGNOSTIC, 59, -5.376174736495e-01, 5.188006683525e-07, 1.4981e+01, 1.8386e-01, \n", " 2DIAGNOSTIC, 60, -5.376174264617e-01, 5.223023048541e-07, 1.5169e+01, 1.8816e-01, \n", " 2DIAGNOSTIC, 61, -5.376161445658e-01, 5.113684545983e-07, 1.5337e+01, 1.6764e-01, \n", " 2DIAGNOSTIC, 62, -5.376163408727e-01, 4.990415968555e-07, 1.5608e+01, 2.7115e-01, \n", " 2DIAGNOSTIC, 63, -5.376146016510e-01, 4.697109213664e-07, 1.5785e+01, 1.7731e-01, \n", " 2DIAGNOSTIC, 64, -5.376138165601e-01, 4.470716611360e-07, 1.5946e+01, 1.6022e-01, \n", " 2DIAGNOSTIC, 65, -5.376133084849e-01, 4.129210965549e-07, 1.6128e+01, 1.8196e-01, \n", " 2DIAGNOSTIC, 66, -5.376134029841e-01, 3.963004734271e-07, 1.6301e+01, 1.7369e-01, \n", " 2DIAGNOSTIC, 67, -5.376128442784e-01, 3.792603685861e-07, 1.6456e+01, 1.5509e-01, \n", " 2DIAGNOSTIC, 68, -5.376123121692e-01, 3.696487565832e-07, 1.6596e+01, 1.3927e-01, \n", " 2DIAGNOSTIC, 69, -5.376119411562e-01, 3.696726329147e-07, 1.6758e+01, 1.6236e-01, \n", " 2DIAGNOSTIC, 70, -5.376111496226e-01, 3.723053054148e-07, 1.6919e+01, 1.6070e-01, \n", " 2DIAGNOSTIC, 71, -5.376114407304e-01, 3.752088276188e-07, 1.7122e+01, 2.0276e-01, \n", " 2DIAGNOSTIC, 72, -5.376109444610e-01, 3.830031210360e-07, 1.7298e+01, 1.7654e-01, \n", " 2DIAGNOSTIC, 73, -5.376104685898e-01, 3.804757558387e-07, 1.7474e+01, 1.7550e-01, \n", " 2DIAGNOSTIC, 74, -5.376099341342e-01, 3.741461269569e-07, 1.7622e+01, 1.4840e-01, \n", " 2DIAGNOSTIC, 75, -5.376094602861e-01, 3.664268485529e-07, 1.7776e+01, 1.5440e-01, \n", " 2DIAGNOSTIC, 76, -5.376097004217e-01, 3.668365117157e-07, 1.7911e+01, 1.3457e-01, \n", " 2DIAGNOSTIC, 77, -5.376095336892e-01, 3.671558582163e-07, 1.8119e+01, 2.0802e-01, \n", " 2DIAGNOSTIC, 78, -5.376091234599e-01, 3.656442498275e-07, 1.8329e+01, 2.1024e-01, \n", " 2DIAGNOSTIC, 79, -5.375976155826e-01, 2.890455070518e-07, 1.8491e+01, 1.6201e-01, \n", " 2DIAGNOSTIC, 80, -5.375974080198e-01, 2.207777474988e-07, 1.8683e+01, 1.9209e-01, \n", " 2DIAGNOSTIC, 81, -5.375979796901e-01, 1.759967496948e-07, 1.8863e+01, 1.7998e-01, \n", " 2DIAGNOSTIC, 82, -5.375980159756e-01, 1.489756694915e-07, 1.9043e+01, 1.7974e-01, \n", " 2DIAGNOSTIC, 83, -5.375986250614e-01, 1.469774571841e-07, 1.9240e+01, 1.9698e-01, \n", " 2DIAGNOSTIC, 84, -5.375968625181e-01, 1.546848640097e-07, 1.9433e+01, 1.9340e-01, \n", " 2DIAGNOSTIC, 85, -5.375965469188e-01, 1.795022595025e-07, 1.9635e+01, 2.0131e-01, \n", " 2DIAGNOSTIC, 86, -5.375948448035e-01, 2.123614638114e-07, 1.9811e+01, 1.7674e-01, \n", " 2DIAGNOSTIC, 87, -5.375949472672e-01, 2.585853996605e-07, 1.9971e+01, 1.6001e-01, \n", " 2DIAGNOSTIC, 88, -5.375944860308e-01, 3.107089746775e-07, 2.0136e+01, 1.6485e-01, \n", " 2DIAGNOSTIC, 89, -5.375946904176e-01, 2.995935224608e-07, 2.0309e+01, 1.7282e-01, \n", " 2DIAGNOSTIC, 90, -5.375942726827e-01, 2.906645507408e-07, 2.0474e+01, 1.6460e-01, \n", " 2DIAGNOSTIC, 91, -5.375939820946e-01, 2.897238707104e-07, 2.0660e+01, 1.8658e-01, \n", " 2DIAGNOSTIC, 92, -5.375942811546e-01, 2.963471317577e-07, 2.0815e+01, 1.5434e-01, \n", " 2DIAGNOSTIC, 93, -5.375935558426e-01, 3.069912943975e-07, 2.1007e+01, 1.9190e-01, \n", " 2DIAGNOSTIC, 94, -5.375944386351e-01, 3.159108195802e-07, 2.1189e+01, 1.8265e-01, \n", " 2DIAGNOSTIC, 95, -5.375939750906e-01, 3.226029893846e-07, 2.1334e+01, 1.4442e-01, \n", " 2DIAGNOSTIC, 96, -5.375931371843e-01, 3.164223846466e-07, 2.1488e+01, 1.5417e-01, \n", " 2DIAGNOSTIC, 97, -5.375937045734e-01, 3.156900502069e-07, 2.1662e+01, 1.7464e-01, \n", " 2DIAGNOSTIC, 98, -5.375934924982e-01, 3.123044314685e-07, 2.1813e+01, 1.5037e-01, \n", " 2DIAGNOSTIC, 99, -5.375939746998e-01, 3.138590516892e-07, 2.2008e+01, 1.9563e-01, \n", " 2DIAGNOSTIC, 100, -5.375930321121e-01, 3.089192639541e-07, 2.2185e+01, 1.7663e-01, \n", " 2DIAGNOSTIC, 101, -5.375927008211e-01, 3.019244832307e-07, 2.2362e+01, 1.7743e-01, \n", " 2DIAGNOSTIC, 102, -5.375912477837e-01, 2.904761466915e-07, 2.2537e+01, 1.7443e-01, \n", " 2DIAGNOSTIC, 103, -5.375915199504e-01, 2.788820572652e-07, 2.2703e+01, 1.6600e-01, \n", " 2DIAGNOSTIC, 104, -5.375905803494e-01, 2.700152922780e-07, 2.2862e+01, 1.5941e-01, \n", " 2DIAGNOSTIC, 105, -5.375910273372e-01, 2.649581509456e-07, 2.2997e+01, 1.3488e-01, \n", " 2DIAGNOSTIC, 106, -5.375904403762e-01, 2.564937863665e-07, 2.3184e+01, 1.8721e-01, \n", " 2DIAGNOSTIC, 107, -5.375890545841e-01, 2.485106557829e-07, 2.3354e+01, 1.6947e-01, \n", " 2DIAGNOSTIC, 108, -5.375886313982e-01, 2.423623614699e-07, 2.3512e+01, 1.5857e-01, \n", " 2DIAGNOSTIC, 109, -5.375890463975e-01, 2.457301629642e-07, 2.3701e+01, 1.8875e-01, \n", " 2DIAGNOSTIC, 110, -5.375893211038e-01, 2.500819504831e-07, 2.3881e+01, 1.8009e-01, \n", " 2DIAGNOSTIC, 111, -5.375884159941e-01, 2.524176132557e-07, 2.4031e+01, 1.4966e-01, \n", " 2DIAGNOSTIC, 112, -5.375888247179e-01, 2.533376353402e-07, 2.4208e+01, 1.7655e-01, \n", " 2DIAGNOSTIC, 113, -5.375905437306e-01, 2.666069586973e-07, 2.4365e+01, 1.5720e-01, \n", " 2DIAGNOSTIC, 114, -5.375899297904e-01, 2.733847373499e-07, 2.4515e+01, 1.5054e-01, \n", " 2DIAGNOSTIC, 115, -5.375897291054e-01, 2.818900448499e-07, 2.4687e+01, 1.7219e-01, \n", " 2DIAGNOSTIC, 116, -5.375901009881e-01, 2.891253828487e-07, 2.4850e+01, 1.6280e-01, \n", " 2DIAGNOSTIC, 117, -5.375922329511e-01, 2.981143613651e-07, 2.5049e+01, 1.9862e-01, \n", " 2DIAGNOSTIC, 118, -5.375930844896e-01, 3.058294192546e-07, 2.5222e+01, 1.7351e-01, \n", " 2DIAGNOSTIC, 119, -5.375921960139e-01, 3.077970084676e-07, 2.5450e+01, 2.2800e-01, \n", " 2DIAGNOSTIC, 120, -5.375912240400e-01, 3.033238502540e-07, 2.5610e+01, 1.5974e-01, \n", " 2DIAGNOSTIC, 121, -5.375914042520e-01, 2.921215825399e-07, 2.5776e+01, 1.6547e-01, \n", " 2DIAGNOSTIC, 122, -5.375909868318e-01, 2.776605406603e-07, 2.5945e+01, 1.6990e-01, \n", " 2DIAGNOSTIC, 123, -5.375904054106e-01, 2.666872820929e-07, 2.6087e+01, 1.4198e-01, \n", " 2DIAGNOSTIC, 124, -5.375900265881e-01, 2.511971005283e-07, 2.6255e+01, 1.6771e-01, \n", " 2DIAGNOSTIC, 125, -5.375902217712e-01, 2.366417009986e-07, 2.6415e+01, 1.6025e-01, \n", " 2DIAGNOSTIC, 126, -5.375893053632e-01, 2.214182615017e-07, 2.6555e+01, 1.3949e-01, \n", " 2DIAGNOSTIC, 127, -5.375904995641e-01, 2.232127352553e-07, 2.6726e+01, 1.7062e-01, \n", " 2DIAGNOSTIC, 128, -5.375908475719e-01, 2.325299561790e-07, 2.6885e+01, 1.5931e-01, \n", " 2DIAGNOSTIC, 129, -5.375914537540e-01, 2.421834540620e-07, 2.7074e+01, 1.8929e-01, \n", " 2DIAGNOSTIC, 130, -5.375917787452e-01, 2.494387670877e-07, 2.7228e+01, 1.5357e-01, \n", " 2DIAGNOSTIC, 131, -5.375909038363e-01, 2.533720833732e-07, 2.7363e+01, 1.3561e-01, \n", " 2DIAGNOSTIC, 132, -5.375908360796e-01, 2.544251121658e-07, 2.7530e+01, 1.6652e-01, \n", " 2DIAGNOSTIC, 133, -5.375905890507e-01, 2.507958656601e-07, 2.7667e+01, 1.3757e-01, \n", " 2DIAGNOSTIC, 134, -5.375905654572e-01, 2.444356925081e-07, 2.7824e+01, 1.5614e-01, \n", " 2DIAGNOSTIC, 135, -5.375909459362e-01, 2.398925633921e-07, 2.7960e+01, 1.3681e-01, \n", " 2DIAGNOSTIC, 136, -5.375903886743e-01, 2.291913164393e-07, 2.8150e+01, 1.8993e-01, \n", " 2DIAGNOSTIC, 137, -5.375907351333e-01, 2.251593073620e-07, 2.8324e+01, 1.7327e-01, \n", " 2DIAGNOSTIC, 138, -5.375884483409e-01, 2.143136551341e-07, 2.8490e+01, 1.6669e-01, \n", " 2DIAGNOSTIC, 139, -5.375882818173e-01, 2.070205863246e-07, 2.8697e+01, 2.0654e-01, \n", " 2DIAGNOSTIC, 140, -5.375872955899e-01, 1.994520245664e-07, 2.8870e+01, 1.7276e-01, \n", " 2DIAGNOSTIC, 141, -5.375873998370e-01, 1.917770387355e-07, 2.9030e+01, 1.6001e-01, \n", " 2DIAGNOSTIC, 142, -5.375870010238e-01, 1.857610798031e-07, 2.9167e+01, 1.3780e-01, \n", " 2DIAGNOSTIC, 143, -5.375867210421e-01, 1.817111791062e-07, 2.9334e+01, 1.6620e-01, \n", " 2DIAGNOSTIC, 144, -5.375932472277e-01, 2.055796059384e-07, 2.9492e+01, 1.5879e-01, \n", " 2DIAGNOSTIC, 145, -5.375950516555e-01, 2.378579131304e-07, 2.9636e+01, 1.4396e-01, \n", " 2DIAGNOSTIC, 146, -5.375961616563e-01, 2.698500824010e-07, 2.9778e+01, 1.4153e-01, \n", " 2DIAGNOSTIC, 147, -5.375978119012e-01, 3.040846678556e-07, 2.9959e+01, 1.8117e-01, \n", " 2DIAGNOSTIC, 148, -5.375965760483e-01, 3.166540354076e-07, 3.0164e+01, 2.0493e-01, \n", " 2DIAGNOSTIC, 149, -5.375971472623e-01, 3.205401459139e-07, 3.0353e+01, 1.8891e-01, \n", " 2DIAGNOSTIC, 150, -5.375962508554e-01, 3.070718215771e-07, 3.0511e+01, 1.5801e-01, \n", " 2DIAGNOSTIC, 151, -5.375958970107e-01, 2.840114884635e-07, 3.0664e+01, 1.5331e-01, \n", " 2DIAGNOSTIC, 152, -5.375956282517e-01, 2.521457165795e-07, 3.0841e+01, 1.7718e-01, \n", " 2DIAGNOSTIC, 153, -5.375958289483e-01, 2.157536912271e-07, 3.1020e+01, 1.7910e-01, \n", " 2DIAGNOSTIC, 154, -5.375953254670e-01, 1.996552908608e-07, 3.1160e+01, 1.3960e-01, \n", " 2DIAGNOSTIC, 155, -5.375949139829e-01, 1.891702520098e-07, 3.1301e+01, 1.4130e-01, \n", " 2DIAGNOSTIC, 156, -5.375947189767e-01, 1.833688599530e-07, 3.1463e+01, 1.6134e-01, \n", " 2DIAGNOSTIC, 157, -5.375955586889e-01, 1.881093490410e-07, 3.1634e+01, 1.7174e-01, \n", " 2DIAGNOSTIC, 158, -5.375951599354e-01, 1.885085346492e-07, 3.1774e+01, 1.3958e-01, \n", " 2DIAGNOSTIC, 159, -5.375949316766e-01, 1.914393495776e-07, 3.1993e+01, 2.1886e-01, \n", " 2DIAGNOSTIC, 160, -5.375950160534e-01, 1.926060848563e-07, 3.2176e+01, 1.8312e-01, \n", " 2DIAGNOSTIC, 161, -5.375945621372e-01, 1.916840024763e-07, 3.2338e+01, 1.6162e-01, \n", " 2DIAGNOSTIC, 162, -5.375940716412e-01, 1.888038882007e-07, 3.2477e+01, 1.3913e-01, \n", " 2DIAGNOSTIC, 163, -5.375936749130e-01, 1.861260835751e-07, 3.2645e+01, 1.6839e-01, \n", " 2DIAGNOSTIC, 164, -5.375938275207e-01, 1.833132436116e-07, 3.2804e+01, 1.5928e-01, \n", " 2DIAGNOSTIC, 165, -5.375933672409e-01, 1.787562186953e-07, 3.2991e+01, 1.8664e-01, \n", " 2DIAGNOSTIC, 166, -5.375928310735e-01, 1.732434903095e-07, 3.3142e+01, 1.5117e-01, \n", " 2DIAGNOSTIC, 167, -5.375916657791e-01, 1.686618617816e-07, 3.3282e+01, 1.3976e-01, \n", " 2DIAGNOSTIC, 168, -5.376031227899e-01, 2.011434557525e-07, 3.3452e+01, 1.7055e-01, \n", " 2DIAGNOSTIC, 169, -5.376040876158e-01, 2.332550507519e-07, 3.3610e+01, 1.5726e-01, \n", " 2DIAGNOSTIC, 170, -5.376058885103e-01, 2.667894524883e-07, 3.3843e+01, 2.3340e-01, \n", " 2DIAGNOSTIC, 171, -5.376060525128e-01, 2.918265428805e-07, 3.4026e+01, 1.8323e-01, \n", " 2DIAGNOSTIC, 172, -5.376045246853e-01, 3.001332243317e-07, 3.4180e+01, 1.5366e-01, \n", " 2DIAGNOSTIC, 173, -5.376036876534e-01, 2.929567155391e-07, 3.4316e+01, 1.3632e-01, \n", " 2DIAGNOSTIC, 174, -5.376042361001e-01, 2.771722813098e-07, 3.4494e+01, 1.7813e-01, \n", " 2DIAGNOSTIC, 175, -5.376048222622e-01, 2.530842053974e-07, 3.4653e+01, 1.5861e-01, \n", " 2DIAGNOSTIC, 176, -5.376046264101e-01, 2.206163933118e-07, 3.4803e+01, 1.5029e-01, \n", " 2DIAGNOSTIC, 177, -5.376061651824e-01, 1.850437643947e-07, 3.5001e+01, 1.9728e-01, \n", " 2DIAGNOSTIC, 178, -5.376050506246e-01, 1.800079718747e-07, 3.5168e+01, 1.6763e-01, \n", " 2DIAGNOSTIC, 179, -5.376040622860e-01, 1.747287151728e-07, 3.5339e+01, 1.7095e-01, \n", " 2DIAGNOSTIC, 180, -5.376040508893e-01, 1.750320114896e-07, 3.5503e+01, 1.6425e-01, \n", " 2DIAGNOSTIC, 181, -5.376029350066e-01, 1.727414921790e-07, 3.5716e+01, 2.1223e-01, \n", " 2DIAGNOSTIC, 182, -5.376025922993e-01, 1.654371506645e-07, 3.5895e+01, 1.7914e-01, \n", " 2DIAGNOSTIC, 183, -5.376020937279e-01, 1.552672957306e-07, 3.6068e+01, 1.7277e-01, \n", " 2DIAGNOSTIC, 184, -5.376006295643e-01, 1.444375706122e-07, 3.6202e+01, 1.3482e-01, \n", " 2DIAGNOSTIC, 185, -5.376001731102e-01, 1.369908956194e-07, 3.6339e+01, 1.3642e-01, \n", " 2DIAGNOSTIC, 186, -5.376005167413e-01, 1.332579869810e-07, 3.6500e+01, 1.6100e-01, \n", " 2DIAGNOSTIC, 187, -5.376003284646e-01, 1.370374524698e-07, 3.6692e+01, 1.9208e-01, \n", " 2DIAGNOSTIC, 188, -5.376001749453e-01, 1.405060356795e-07, 3.6872e+01, 1.7992e-01, \n", " 2DIAGNOSTIC, 189, -5.375991405659e-01, 1.411213376278e-07, 3.7055e+01, 1.8285e-01, \n", " 2DIAGNOSTIC, 190, -5.375986958181e-01, 1.432639202825e-07, 3.7207e+01, 1.5224e-01, \n", " 2DIAGNOSTIC, 191, -5.375983377897e-01, 1.435848105222e-07, 3.7352e+01, 1.4543e-01, \n", " 2DIAGNOSTIC, 192, -5.375982002325e-01, 1.447591384341e-07, 3.7512e+01, 1.5944e-01, \n", " 2DIAGNOSTIC, 193, -5.375979566861e-01, 1.460390568328e-07, 3.7687e+01, 1.7532e-01, \n", " 2DIAGNOSTIC, 194, -5.375953265560e-01, 1.380673772030e-07, 3.7844e+01, 1.5655e-01, \n", " 2DIAGNOSTIC, 195, -5.375944034226e-01, 1.291434532178e-07, 3.8012e+01, 1.6878e-01, \n", " 2DIAGNOSTIC, 196, -5.375941270600e-01, 1.237616150725e-07, 3.8164e+01, 1.5175e-01, \n", " 2DIAGNOSTIC, 197, -5.375940897469e-01, 1.214275192722e-07, 3.8354e+01, 1.8964e-01, \n", " 2DIAGNOSTIC, 198, -5.375931592067e-01, 1.201624207827e-07, 3.8545e+01, 1.9131e-01, \n", " 2DIAGNOSTIC, 199, -5.375927656856e-01, 1.192618599094e-07, 3.8734e+01, 1.8922e-01, \n", " 2DIAGNOSTIC, 200, -5.375921940530e-01, 1.197154439686e-07, 3.8891e+01, 1.5694e-01, \n", " 2DIAGNOSTIC, 201, -5.375915675313e-01, 1.213062734099e-07, 3.9046e+01, 1.5504e-01, \n", " 2DIAGNOSTIC, 202, -5.375910918270e-01, 1.247952029406e-07, 3.9193e+01, 1.4702e-01, \n", " 2DIAGNOSTIC, 203, -5.375912754692e-01, 1.314676908205e-07, 3.9359e+01, 1.6532e-01, \n", " 2DIAGNOSTIC, 204, -5.375915831348e-01, 1.345477020648e-07, 3.9511e+01, 1.5208e-01, \n", " 2DIAGNOSTIC, 205, -5.375912795374e-01, 1.364940386966e-07, 3.9678e+01, 1.6752e-01, \n", " 2DIAGNOSTIC, 206, -5.375898046006e-01, 1.357798359849e-07, 3.9841e+01, 1.6272e-01, \n", " 2DIAGNOSTIC, 207, -5.375877384553e-01, 1.316834192964e-07, 4.0056e+01, 2.1504e-01, \n", " 2DIAGNOSTIC, 208, -5.375879111255e-01, 1.279124724612e-07, 4.0218e+01, 1.6187e-01, \n", " 2DIAGNOSTIC, 209, -5.375863341834e-01, 1.214839693850e-07, 4.0358e+01, 1.4030e-01, \n", " 2DIAGNOSTIC, 210, -5.375860328077e-01, 1.160060041300e-07, 4.0497e+01, 1.3832e-01, \n", " 2DIAGNOSTIC, 211, -5.375859338218e-01, 1.123338032429e-07, 4.0660e+01, 1.6333e-01, \n", " 2DIAGNOSTIC, 212, -5.375870004472e-01, 1.139279268971e-07, 4.0907e+01, 2.4682e-01, \n", " 2DIAGNOSTIC, 213, -5.375870627780e-01, 1.194798516660e-07, 4.1074e+01, 1.6682e-01, \n", " 2DIAGNOSTIC, 214, -5.375864720168e-01, 1.271730634923e-07, 4.1201e+01, 1.2717e-01, \n", " 2DIAGNOSTIC, 215, -5.375853051215e-01, 1.334336654423e-07, 4.1366e+01, 1.6556e-01, \n", " 2DIAGNOSTIC, 216, -5.375853553200e-01, 1.377141563190e-07, 4.1506e+01, 1.3947e-01, \n", " 2DIAGNOSTIC, 217, -5.375848661561e-01, 1.364851991694e-07, 4.1665e+01, 1.5899e-01, \n", " 2DIAGNOSTIC, 218, -5.375849283225e-01, 1.369007503142e-07, 4.1797e+01, 1.3194e-01, \n", " 2DIAGNOSTIC, 219, -5.375844588899e-01, 1.333282768192e-07, 4.1949e+01, 1.5202e-01, \n", " 2DIAGNOSTIC, 220, -5.375846008375e-01, 1.306738001694e-07, 4.2103e+01, 1.5403e-01, \n", " 2DIAGNOSTIC, 221, -5.375842548894e-01, 1.282322184253e-07, 4.2252e+01, 1.4964e-01, \n", " 2DIAGNOSTIC, 222, -5.375840723930e-01, 1.294094077375e-07, 4.2458e+01, 2.0587e-01, \n", " 2DIAGNOSTIC, 223, -5.375848464090e-01, 1.339335472658e-07, 4.2630e+01, 1.7173e-01, \n", " 2DIAGNOSTIC, 224, -5.375832127547e-01, 1.340238091002e-07, 4.2780e+01, 1.4964e-01, \n", " 2DIAGNOSTIC, 225, -5.375835671736e-01, 1.330935447729e-07, 4.2972e+01, 1.9200e-01, \n", " 2DIAGNOSTIC, 226, -5.375837545611e-01, 1.335249120923e-07, 4.3141e+01, 1.6989e-01, \n", " 2DIAGNOSTIC, 227, -5.375825938322e-01, 1.307410376324e-07, 4.3285e+01, 1.4395e-01, \n", " 2DIAGNOSTIC, 228, -5.375823325457e-01, 1.285381554311e-07, 4.3418e+01, 1.3212e-01, \n", " 2DIAGNOSTIC, 229, -5.375834814962e-01, 1.290128021194e-07, 4.3613e+01, 1.9562e-01, \n", " 2DIAGNOSTIC, 230, -5.375837667008e-01, 1.313485869601e-07, 4.3777e+01, 1.6374e-01, \n", " 2DIAGNOSTIC, 231, -5.375833599653e-01, 1.325946649222e-07, 4.3917e+01, 1.3997e-01, \n", " 2DIAGNOSTIC, 232, -5.375830631136e-01, 1.332757761010e-07, 4.4071e+01, 1.5426e-01, \n", " 2DIAGNOSTIC, 233, -5.375827431856e-01, 1.355071927419e-07, 4.4243e+01, 1.7223e-01, \n", " 2DIAGNOSTIC, 234, -5.375822682730e-01, 1.329478691190e-07, 4.4380e+01, 1.3647e-01, \n", " 2DIAGNOSTIC, 235, -5.375806789995e-01, 1.278648884490e-07, 4.4551e+01, 1.7135e-01, \n", " 2DIAGNOSTIC, 236, -5.375802511292e-01, 1.232191194044e-07, 4.4700e+01, 1.4875e-01, \n", " 2DIAGNOSTIC, 237, -5.375793492239e-01, 1.151811066793e-07, 4.4861e+01, 1.6076e-01, \n", " 2DIAGNOSTIC, 238, -5.375791212581e-01, 1.079049879197e-07, 4.5023e+01, 1.6192e-01, \n", " 2DIAGNOSTIC, 239, -5.375765583344e-01, 1.000395901526e-07, 4.5201e+01, 1.7817e-01, \n", " 2DIAGNOSTIC, 240, -5.375759833562e-01, 9.501753432326e-08, 4.5341e+01, 1.4007e-01, \n", " 2DIAGNOSTIC, 241, -5.375769308096e-01, 9.486852313445e-08, 4.5509e+01, 1.6833e-01, \n", " 2DIAGNOSTIC, 242, -5.375782180385e-01, 1.003246647719e-07, 4.5701e+01, 1.9145e-01, \n", " 2DIAGNOSTIC, 243, -5.375775036105e-01, 1.064512291345e-07, 4.5883e+01, 1.8196e-01, \n", " 2DIAGNOSTIC, 244, -5.375766167358e-01, 1.122265792831e-07, 4.6028e+01, 1.4586e-01, \n", " 2DIAGNOSTIC, 245, -5.375759875823e-01, 1.150455891117e-07, 4.6176e+01, 1.4780e-01, \n", " 2DIAGNOSTIC, 246, -5.375770461303e-01, 1.205485499903e-07, 4.6331e+01, 1.5424e-01, \n", " 2DIAGNOSTIC, 247, -5.375793955895e-01, 1.297263101888e-07, 4.6535e+01, 2.0474e-01, \n", " 2DIAGNOSTIC, 248, -5.375791532733e-01, 1.377955140269e-07, 4.6692e+01, 1.5699e-01, \n", " 2DIAGNOSTIC, 249, -5.375786291570e-01, 1.385749207935e-07, 4.6856e+01, 1.6364e-01, \n", " 2DIAGNOSTIC, 250, -5.375782119093e-01, 1.362737871869e-07, 4.7019e+01, 1.6327e-01, \n", "DIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST\n", " 2DIAGNOSTIC, 1, -4.700513666530e-01, 1.797693134862e+308, 5.0541e+01, 3.5218e+00, \n", " 2DIAGNOSTIC, 2, -4.703312910418e-01, 1.797693134862e+308, 5.1428e+01, 8.8730e-01, \n", " 2DIAGNOSTIC, 3, -4.705412559848e-01, 1.797693134862e+308, 5.2288e+01, 8.5974e-01, \n", " 2DIAGNOSTIC, 4, -4.706771329736e-01, 1.797693134862e+308, 5.3097e+01, 8.0921e-01, \n", " 2DIAGNOSTIC, 5, -4.709083121561e-01, 1.797693134862e+308, 5.3915e+01, 8.1809e-01, \n", " 2DIAGNOSTIC, 6, -4.710547452032e-01, 1.797693134862e+308, 5.4954e+01, 1.0385e+00, \n", " 2DIAGNOSTIC, 7, -4.711814029449e-01, 1.797693134862e+308, 5.6050e+01, 1.0966e+00, \n", " 2DIAGNOSTIC, 8, -4.713211030902e-01, 1.797693134862e+308, 5.6885e+01, 8.3497e-01, \n", " 2DIAGNOSTIC, 9, -4.713840725895e-01, 1.797693134862e+308, 5.7744e+01, 8.5883e-01, \n", " 2DIAGNOSTIC, 10, -4.715498739890e-01, 1.978470544600e-04, 5.9153e+01, 1.4088e+00, \n", " 2DIAGNOSTIC, 11, -4.715931324866e-01, 1.594074914670e-04, 5.9969e+01, 8.1593e-01, \n", " 2DIAGNOSTIC, 12, -4.717952415264e-01, 1.374807313615e-04, 6.0814e+01, 8.4520e-01, \n", " 2DIAGNOSTIC, 13, -4.718957042546e-01, 1.209626512942e-04, 6.1636e+01, 8.2221e-01, \n", " 2DIAGNOSTIC, 14, -4.719439865103e-01, 1.037746352003e-04, 6.2585e+01, 9.4833e-01, \n", " 2DIAGNOSTIC, 15, -4.719433659732e-01, 8.886865704286e-05, 6.3718e+01, 1.1332e+00, \n", " 2DIAGNOSTIC, 16, -4.719380725524e-01, 7.316468958833e-05, 6.5132e+01, 1.4143e+00, \n", " 2DIAGNOSTIC, 17, -4.719377938413e-01, 5.711565291695e-05, 6.6590e+01, 1.4576e+00, \n", " 2DIAGNOSTIC, 18, -4.719378102242e-01, 4.236925636499e-05, 6.7652e+01, 1.0625e+00, \n", " 2DIAGNOSTIC, 19, -4.719377020034e-01, 2.733950596132e-05, 6.8636e+01, 9.8330e-01, \n", " 2DIAGNOSTIC, 20, -4.719376806478e-01, 1.650831139213e-05, 6.9716e+01, 1.0800e+00, \n", " 2DIAGNOSTIC, 21, -4.719376307642e-01, 6.454422911445e-06, 7.0695e+01, 9.7988e-01, \n", " 2DIAGNOSTIC, 22, -4.719375208578e-01, 2.327090553887e-06, 7.1552e+01, 8.5702e-01, \n", " 2DIAGNOSTIC, 23, -4.719374800630e-01, 1.070091029745e-06, 7.2492e+01, 9.3937e-01, \n", " 2DIAGNOSTIC, 24, -4.719374951887e-01, 1.159228170546e-06, 7.3310e+01, 8.1819e-01, \n", " 2DIAGNOSTIC, 25, -4.719374438019e-01, 1.244294881422e-06, 7.4158e+01, 8.4770e-01, \n", " 2DIAGNOSTIC, 26, -4.719375434332e-01, 1.205361279261e-06, 7.4987e+01, 8.2929e-01, \n", " 2DIAGNOSTIC, 27, -4.719372776110e-01, 1.158895090607e-06, 7.5790e+01, 8.0345e-01, \n", " 2DIAGNOSTIC, 28, -4.719373045806e-01, 1.118832152799e-06, 7.6704e+01, 9.1324e-01, \n", " 2DIAGNOSTIC, 29, -4.719373675324e-01, 1.082225833712e-06, 7.7671e+01, 9.6700e-01, \n", " 2DIAGNOSTIC, 30, -4.719374080641e-01, 1.049797259352e-06, 7.8643e+01, 9.7273e-01, \n", " 2DIAGNOSTIC, 31, -4.719374156190e-01, 1.019761629556e-06, 7.9640e+01, 9.9676e-01, \n", " 2DIAGNOSTIC, 32, -4.719374027112e-01, 9.900767391977e-07, 8.0583e+01, 9.4314e-01, \n", " 2DIAGNOSTIC, 33, -4.719373382286e-01, 9.607520405699e-07, 8.1516e+01, 9.3261e-01, \n", " 2DIAGNOSTIC, 34, -4.719371638211e-01, 9.306762020211e-07, 8.2472e+01, 9.5570e-01, \n", " 2DIAGNOSTIC, 35, -4.719372049855e-01, 9.026266618965e-07, 8.3494e+01, 1.0226e+00, \n", " 2DIAGNOSTIC, 36, -4.719371598652e-01, 8.777721113538e-07, 8.4419e+01, 9.2454e-01, \n", " 2DIAGNOSTIC, 37, -4.719369818753e-01, 8.476436661013e-07, 8.5377e+01, 9.5818e-01, \n", " 2DIAGNOSTIC, 38, -4.719369940265e-01, 8.210163935964e-07, 8.6223e+01, 8.4600e-01, \n", " 2DIAGNOSTIC, 39, -4.719369586206e-01, 7.977397671610e-07, 8.7052e+01, 8.2943e-01, \n", " 2DIAGNOSTIC, 40, -4.719370498339e-01, 7.793195071944e-07, 8.8014e+01, 9.6132e-01, \n", " 2DIAGNOSTIC, 41, -4.719370720972e-01, 7.637295615023e-07, 8.9023e+01, 1.0094e+00, \n", " 2DIAGNOSTIC, 42, -4.719370080337e-01, 7.490265051882e-07, 8.9941e+01, 9.1838e-01, \n", " 2DIAGNOSTIC, 43, -4.719369115435e-01, 7.337151788599e-07, 9.0888e+01, 9.4624e-01, \n", " 2DIAGNOSTIC, 44, -4.719368696868e-01, 7.167266194603e-07, 9.1792e+01, 9.0413e-01, \n", " 2DIAGNOSTIC, 45, -4.719368276462e-01, 7.010712678793e-07, 9.2608e+01, 8.1581e-01, \n", " 2DIAGNOSTIC, 46, -4.719367376651e-01, 6.849620349109e-07, 9.3551e+01, 9.4311e-01, \n", " 2DIAGNOSTIC, 47, -4.719367581276e-01, 6.682244896271e-07, 9.4491e+01, 9.4055e-01, \n", " 2DIAGNOSTIC, 48, -4.719366611184e-01, 6.520003130797e-07, 9.5436e+01, 9.4477e-01, \n", " 2DIAGNOSTIC, 49, -4.719366295337e-01, 6.366637681984e-07, 9.6330e+01, 8.9342e-01, \n", " 2DIAGNOSTIC, 50, -4.719366786926e-01, 6.248410217742e-07, 9.7313e+01, 9.8347e-01, \n", " 2DIAGNOSTIC, 51, -4.719365818897e-01, 6.136978157392e-07, 9.8261e+01, 9.4823e-01, \n", " 2DIAGNOSTIC, 52, -4.719364901272e-01, 6.022222257575e-07, 9.9169e+01, 9.0806e-01, \n", " 2DIAGNOSTIC, 53, -4.719363847169e-01, 5.898591098827e-07, 1.0020e+02, 1.0326e+00, \n", " 2DIAGNOSTIC, 54, -4.719363789153e-01, 5.784556089822e-07, 1.0119e+02, 9.8588e-01, \n", " 2DIAGNOSTIC, 55, -4.719363498543e-01, 5.677132052725e-07, 1.0227e+02, 1.0822e+00, \n", " 2DIAGNOSTIC, 56, -4.719364651275e-01, 5.586574712002e-07, 1.0326e+02, 9.9106e-01, \n", " 2DIAGNOSTIC, 57, -4.719364307653e-01, 5.507149438526e-07, 1.0437e+02, 1.1086e+00, \n", " 2DIAGNOSTIC, 58, -4.719363652582e-01, 5.421280395435e-07, 1.0540e+02, 1.0332e+00, \n", " 2DIAGNOSTIC, 59, -4.719363183056e-01, 5.336575572799e-07, 1.0629e+02, 8.8917e-01, \n", " 2DIAGNOSTIC, 60, -4.719363416731e-01, 5.267465752329e-07, 1.0714e+02, 8.4380e-01, \n", " 2DIAGNOSTIC, 61, -4.719363667062e-01, 5.196748435257e-07, 1.0798e+02, 8.4887e-01, \n", " 2DIAGNOSTIC, 62, -4.719364675658e-01, 5.131279845125e-07, 1.0899e+02, 1.0016e+00, \n", " 2DIAGNOSTIC, 63, -4.719364950455e-01, 5.060645470664e-07, 1.0984e+02, 8.5485e-01, \n", " 2DIAGNOSTIC, 64, -4.719365061808e-01, 4.992120806388e-07, 1.1070e+02, 8.5968e-01, \n", " 2DIAGNOSTIC, 65, -4.719366425136e-01, 4.933398239058e-07, 1.1197e+02, 1.2655e+00, \n", " 2DIAGNOSTIC, 66, -4.719365294471e-01, 4.872577178683e-07, 1.1298e+02, 1.0183e+00, \n", " 2DIAGNOSTIC, 67, -4.719365464889e-01, 4.807516614976e-07, 1.1393e+02, 9.4774e-01, \n", " 2DIAGNOSTIC, 68, -4.719365157606e-01, 4.730376805973e-07, 1.1492e+02, 9.8583e-01, \n", " 2DIAGNOSTIC, 69, -4.719365081226e-01, 4.645779288562e-07, 1.1599e+02, 1.0679e+00, \n", " 2DIAGNOSTIC, 70, -4.719365572006e-01, 4.566472950086e-07, 1.1708e+02, 1.0972e+00, \n", " 2DIAGNOSTIC, 71, -4.719365255681e-01, 4.486586309763e-07, 1.1826e+02, 1.1750e+00, \n", " 2DIAGNOSTIC, 72, -4.719364244153e-01, 4.408693438217e-07, 1.1930e+02, 1.0418e+00, \n", " 2DIAGNOSTIC, 73, -4.719363680892e-01, 4.331863579076e-07, 1.2019e+02, 8.8958e-01, \n", " 2DIAGNOSTIC, 74, -4.719363797693e-01, 4.261164716982e-07, 1.2104e+02, 8.5301e-01, \n", " 2DIAGNOSTIC, 75, -4.719363995023e-01, 4.208600843433e-07, 1.2216e+02, 1.1181e+00, \n", " 2DIAGNOSTIC, 76, -4.719363332003e-01, 4.146361059568e-07, 1.2312e+02, 9.5996e-01, \n", " 2DIAGNOSTIC, 77, -4.719362946953e-01, 4.088427295965e-07, 1.2410e+02, 9.8379e-01, \n", " 2DIAGNOSTIC, 78, -4.719362040557e-01, 4.027021961815e-07, 1.2501e+02, 9.0262e-01, \n", " 2DIAGNOSTIC, 79, -4.719361888923e-01, 3.970304240791e-07, 1.2598e+02, 9.7664e-01, \n", " 2DIAGNOSTIC, 80, -4.719361587273e-01, 3.921778140414e-07, 1.2700e+02, 1.0120e+00, \n", " 2DIAGNOSTIC, 81, -4.719361764519e-01, 3.878996358789e-07, 1.2800e+02, 1.0074e+00, \n", " 2DIAGNOSTIC, 82, -4.719361396010e-01, 3.832042372795e-07, 1.2891e+02, 9.0998e-01, \n", " 2DIAGNOSTIC, 83, -4.719360600263e-01, 3.781121185129e-07, 1.2973e+02, 8.1244e-01, \n", " 2DIAGNOSTIC, 84, -4.719361775629e-01, 3.745809060464e-07, 1.3061e+02, 8.8822e-01, \n", " 2DIAGNOSTIC, 85, -4.719359726364e-01, 3.701959556384e-07, 1.3153e+02, 9.1392e-01, \n", " 2DIAGNOSTIC, 86, -4.719358468509e-01, 3.650076629436e-07, 1.3255e+02, 1.0185e+00, \n", " 2DIAGNOSTIC, 87, -4.719358538268e-01, 3.602416010409e-07, 1.3356e+02, 1.0128e+00, \n", " 2DIAGNOSTIC, 88, -4.719357999131e-01, 3.550998820823e-07, 1.3456e+02, 1.0048e+00, \n", " 2DIAGNOSTIC, 89, -4.719359952966e-01, 3.519134623431e-07, 1.3561e+02, 1.0481e+00, \n", " 2DIAGNOSTIC, 90, -4.719359241164e-01, 3.486279153333e-07, 1.3670e+02, 1.0879e+00, \n", " 2DIAGNOSTIC, 91, -4.719359561796e-01, 3.462742626179e-07, 1.3766e+02, 9.5920e-01, \n", " 2DIAGNOSTIC, 92, -4.719358339894e-01, 3.432721010447e-07, 1.3872e+02, 1.0566e+00, \n", " 2DIAGNOSTIC, 93, -4.719357620246e-01, 3.395695077537e-07, 1.3972e+02, 1.0073e+00, \n", " 2DIAGNOSTIC, 94, -4.719357539051e-01, 3.369120002792e-07, 1.4062e+02, 8.9765e-01, \n", " 2DIAGNOSTIC, 95, -4.719357454583e-01, 3.331132041786e-07, 1.4148e+02, 8.5897e-01, \n", " 2DIAGNOSTIC, 96, -4.719357261305e-01, 3.286674946038e-07, 1.4249e+02, 1.0135e+00, \n", " 2DIAGNOSTIC, 97, -4.719358815285e-01, 3.256221446576e-07, 1.4346e+02, 9.6452e-01, \n", " 2DIAGNOSTIC, 98, -4.719350431745e-01, 3.173308199735e-07, 1.4462e+02, 1.1666e+00, \n", " 2DIAGNOSTIC, 99, -4.719350899135e-01, 3.115511708219e-07, 1.4550e+02, 8.7993e-01, \n", " 2DIAGNOSTIC, 100, -4.719349721738e-01, 3.056279772196e-07, 1.4681e+02, 1.3032e+00, \n", " Elapsed time (stage 1): 1.4826e+02\n", "\n", "\n", "Stage 2\n", " iterations = 50x10x0\n", " convergence threshold = 1.0000e-09\n", " convergence window size = 15\n", " number of levels = 3\n", " using the CC metric (radius = 4, weight = 5.0000e-01)\n", " preprocessing: winsorizing the image intensities\n", " preprocessing: histogram matching the images\n", " using the CC metric (radius = 4, weight = 5.0000e-01)\n", " preprocessing: winsorizing the image intensities\n", " preprocessing: histogram matching the images\n", " Shrink factors (level 1 out of 3): [4, 4, 4]\n", " Shrink factors (level 2 out of 3): [2, 2, 2]\n", " Shrink factors (level 3 out of 3): [1, 1, 1]\n", " smoothing sigmas per level: [2, 1, 0]\n", " Using default NONE metricSamplingStrategy \n", "\n", "*** Running SyN registration (varianceForUpdateField = 3.0000e+00, varianceForTotalField = 0.0000e+00) ***\n", "\n", "XXDIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST\n", " 1DIAGNOSTIC, 1, -4.234589754383e-01, 1.797693134862e+308, 5.2055e+00, 5.2055e+00, \n", " 1DIAGNOSTIC, 2, -4.278472288749e-01, 1.797693134862e+308, 6.6175e+00, 1.4119e+00, \n", " 1DIAGNOSTIC, 3, -4.322648513882e-01, 1.797693134862e+308, 9.3000e+00, 2.6825e+00, \n", " 1DIAGNOSTIC, 4, -4.372516763789e-01, 1.797693134862e+308, 1.0552e+01, 1.2518e+00, \n", " 1DIAGNOSTIC, 5, -4.413636722155e-01, 1.797693134862e+308, 1.1803e+01, 1.2509e+00, \n", " 1DIAGNOSTIC, 6, -4.454195465284e-01, 1.797693134862e+308, 1.3469e+01, 1.6665e+00, \n", " 1DIAGNOSTIC, 7, -4.484376916133e-01, 1.797693134862e+308, 1.6497e+01, 3.0275e+00, \n", " 1DIAGNOSTIC, 8, -4.512899319036e-01, 1.797693134862e+308, 1.7842e+01, 1.3454e+00, \n", " 1DIAGNOSTIC, 9, -4.530936515465e-01, 1.797693134862e+308, 1.9075e+01, 1.2327e+00, \n", " 1DIAGNOSTIC, 10, -4.553215662375e-01, 1.797693134862e+308, 2.0526e+01, 1.4514e+00, \n", " 1DIAGNOSTIC, 11, -4.572888328089e-01, 1.797693134862e+308, 2.1756e+01, 1.2297e+00, \n", " 1DIAGNOSTIC, 12, -4.592668263317e-01, 1.797693134862e+308, 2.4922e+01, 3.1662e+00, \n", " 1DIAGNOSTIC, 13, -4.608719308295e-01, 1.797693134862e+308, 2.7110e+01, 2.1878e+00, \n", " 1DIAGNOSTIC, 14, -4.626631661951e-01, 1.797693134862e+308, 2.9692e+01, 2.5817e+00, \n", " 1DIAGNOSTIC, 15, -4.638786977212e-01, 3.629722417312e-03, 3.1071e+01, 1.3793e+00, \n", " 1DIAGNOSTIC, 16, -4.652642566345e-01, 3.067782340778e-03, 3.2398e+01, 1.3276e+00, \n", " 1DIAGNOSTIC, 17, -4.667293703023e-01, 2.592006265296e-03, 3.4046e+01, 1.6476e+00, \n", " 1DIAGNOSTIC, 18, -4.679441244918e-01, 2.193685279438e-03, 3.5445e+01, 1.3989e+00, \n", " 1DIAGNOSTIC, 19, -4.687213657620e-01, 1.874091077861e-03, 3.8044e+01, 2.5994e+00, \n", " 1DIAGNOSTIC, 20, -4.700330027122e-01, 1.622408736062e-03, 3.9253e+01, 1.2087e+00, \n", " 1DIAGNOSTIC, 21, -4.709612339334e-01, 1.426677093310e-03, 4.0428e+01, 1.1752e+00, \n", " 1DIAGNOSTIC, 22, -4.716623228719e-01, 1.259864550770e-03, 4.1716e+01, 1.2879e+00, \n", " 1DIAGNOSTIC, 23, -4.726044833996e-01, 1.124304152946e-03, 4.3426e+01, 1.7094e+00, \n", " 1DIAGNOSTIC, 24, -4.732236624356e-01, 9.947278666121e-04, 4.4900e+01, 1.4740e+00, \n", " 1DIAGNOSTIC, 25, -4.741714784046e-01, 8.867180632732e-04, 4.6138e+01, 1.2382e+00, \n", " 1DIAGNOSTIC, 26, -4.753584191019e-01, 8.000127568849e-04, 4.7493e+01, 1.3553e+00, \n", " 1DIAGNOSTIC, 27, -4.763155650763e-01, 7.308938699132e-04, 4.8637e+01, 1.1437e+00, \n", " 1DIAGNOSTIC, 28, -4.771920951766e-01, 6.722875214039e-04, 5.0299e+01, 1.6618e+00, \n", " 1DIAGNOSTIC, 29, -4.780042645086e-01, 6.265139162537e-04, 5.2024e+01, 1.7250e+00, \n", " 1DIAGNOSTIC, 30, -4.788734715358e-01, 5.858775635680e-04, 5.3306e+01, 1.2822e+00, \n", " 1DIAGNOSTIC, 31, -4.797165213162e-01, 5.525809844118e-04, 5.4588e+01, 1.2822e+00, \n", " 1DIAGNOSTIC, 32, -4.806078702232e-01, 5.282447739261e-04, 5.5947e+01, 1.3586e+00, \n", " 1DIAGNOSTIC, 33, -4.815986838009e-01, 5.103887224803e-04, 5.7254e+01, 1.3077e+00, \n", " 1DIAGNOSTIC, 34, -4.823627078366e-01, 4.900793521743e-04, 5.8520e+01, 1.2655e+00, \n", " 1DIAGNOSTIC, 35, -4.826963042369e-01, 4.692795646565e-04, 6.0939e+01, 2.4193e+00, \n", " 1DIAGNOSTIC, 36, -4.833730138766e-01, 4.481409053942e-04, 6.2467e+01, 1.5274e+00, \n", " 1DIAGNOSTIC, 37, -4.833823787206e-01, 4.168686670511e-04, 6.3826e+01, 1.3596e+00, \n", " 1DIAGNOSTIC, 38, -4.838682608626e-01, 3.851505008229e-04, 6.5094e+01, 1.2679e+00, \n", " 1DIAGNOSTIC, 39, -4.840300533673e-01, 3.466802287668e-04, 6.8077e+01, 2.9829e+00, \n", " 1DIAGNOSTIC, 40, -4.844999288215e-01, 3.097298816542e-04, 6.9505e+01, 1.4284e+00, \n", " 1DIAGNOSTIC, 41, -4.849402269186e-01, 2.774966725657e-04, 7.0752e+01, 1.2467e+00, \n", " 1DIAGNOSTIC, 42, -4.851155589164e-01, 2.458502198368e-04, 7.2075e+01, 1.3224e+00, \n", " 1DIAGNOSTIC, 43, -4.855030077509e-01, 2.172149797169e-04, 7.4099e+01, 2.0240e+00, \n", " 1DIAGNOSTIC, 44, -4.856606199315e-01, 1.895566843640e-04, 7.5946e+01, 1.8473e+00, \n", " 1DIAGNOSTIC, 45, -4.859119223313e-01, 1.651775036497e-04, 7.7195e+01, 1.2492e+00, \n", " 1DIAGNOSTIC, 46, -4.863229910519e-01, 1.458158917353e-04, 7.8882e+01, 1.6867e+00, \n", " 1DIAGNOSTIC, 47, -4.864736938439e-01, 1.298391911202e-04, 8.0303e+01, 1.4213e+00, \n", " 1DIAGNOSTIC, 48, -4.868194539983e-01, 1.202257259347e-04, 8.1664e+01, 1.3614e+00, \n", " 1DIAGNOSTIC, 49, -4.869135334630e-01, 1.129155630119e-04, 8.3118e+01, 1.4536e+00, \n", " 1DIAGNOSTIC, 50, -4.872942457930e-01, 1.068202867904e-04, 8.4498e+01, 1.3804e+00, \n", "XXDIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST\n", " 1DIAGNOSTIC, 1, -4.955191817152e-01, 1.797693134862e+308, 1.0176e+02, 1.7257e+01, \n", " 1DIAGNOSTIC, 2, -4.974512849183e-01, 1.797693134862e+308, 1.1393e+02, 1.2176e+01, \n", " 1DIAGNOSTIC, 3, -4.994861466982e-01, 1.797693134862e+308, 1.4798e+02, 3.4046e+01, \n", " 1DIAGNOSTIC, 4, -5.016186020828e-01, 1.797693134862e+308, 1.5893e+02, 1.0949e+01, \n", " 1DIAGNOSTIC, 5, -5.034680120602e-01, 1.797693134862e+308, 1.6895e+02, 1.0023e+01, \n", " 1DIAGNOSTIC, 6, -5.052220148690e-01, 1.797693134862e+308, 1.7863e+02, 9.6827e+00, \n", " 1DIAGNOSTIC, 7, -5.065216692225e-01, 1.797693134862e+308, 1.8786e+02, 9.2259e+00, \n", " 1DIAGNOSTIC, 8, -5.079557973214e-01, 1.797693134862e+308, 1.9686e+02, 9.0047e+00, \n", " 1DIAGNOSTIC, 9, -5.090849755324e-01, 1.797693134862e+308, 2.0602e+02, 9.1576e+00, \n", " 1DIAGNOSTIC, 10, -5.104333514778e-01, 1.797693134862e+308, 2.1817e+02, 1.2147e+01, \n", " Elapsed time (stage 2): 232.2\n", "\n", "\n", "Total elapsed time: 521.2\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "/opt/ants-2.3.1//antsApplyTransforms -d 3 -i OASIS/MICCAI2012-Multi-Atlas-Challenge-Data/T_template0_BrainCerebellumProbabilityMask.nii.gz -o ANTS_Stripped_BrainExtractionPriorWarped.nii.gz -r ds000102/sub-08/anat/sub-08_T1w.nii.gz -n Gaussian -t [ANTS_Stripped_BrainExtractionPrior0GenericAffine.mat,1] -t ANTS_Stripped_BrainExtractionPrior1InverseWarp.nii.gz --float 0 --verbose 1\n", "Using double precision for computations.\n", "Input scalar image: OASIS/MICCAI2012-Multi-Atlas-Challenge-Data/T_template0_BrainCerebellumProbabilityMask.nii.gz\n", "Reference image: ds000102/sub-08/anat/sub-08_T1w.nii.gz\n", "=============================================================================\n", "The composite transform comprises the following transforms (in order): \n", " 1. ANTS_Stripped_BrainExtractionPrior1InverseWarp.nii.gz (type = DisplacementFieldTransform)\n", " 2. inverse of ANTS_Stripped_BrainExtractionPrior0GenericAffine.mat (type = AffineTransform)\n", "=============================================================================\n", "Default pixel value: 0\n", "Interpolation type: GaussianInterpolateImageFunction\n", "Output warped image: ANTS_Stripped_BrainExtractionPriorWarped.nii.gz\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "/opt/ants-2.3.1//ThresholdImage 3 ANTS_Stripped_BrainExtractionPriorWarped.nii.gz ANTS_Stripped_BrainExtractionPriorWarped.nii.gz 0.5 1 1 0\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "/opt/ants-2.3.1//ImageMath 3 ANTS_Stripped_BrainExtractionMask.nii.gz MD ANTS_Stripped_BrainExtractionPriorWarped.nii.gz 2\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "/opt/ants-2.3.1//ImageMath 3 ANTS_Stripped_BrainExtractionMask.nii.gz GetLargestComponent ANTS_Stripped_BrainExtractionMask.nii.gz\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "/opt/ants-2.3.1//Atropos -d 3 -o ANTS_Stripped_BrainExtractionSegmentation.nii.gz -a ANTS_Stripped_N4Corrected0.nii.gz -x ANTS_Stripped_BrainExtractionMask.nii.gz -i kmeans[3] -c [3,0.0] -m [0.1,1x1x1] -k Gaussian -r 1 --verbose 1\n", "\n", "Running Atropos for 3-dimensional images.\n", "\n", "Progress: \n", " Iteration 0 (of 3): posterior probability = 0 (annealing temperature = 1)\n", " Iteration 1 (of 3): posterior probability = 0.953876 (annealing temperature = 1)\n", "\n", "Writing output:\n", "\n", " AtroposSegmentationImageFilter (0x35e83f0)\n", " RTTI typeinfo: itk::ants::AtroposSegmentationImageFilter, itk::Image, itk::Image >\n", " Reference Count: 1\n", " Modified Time: 9117948\n", " Debug: Off\n", " Object Name: \n", " Observers: \n", " IterationEvent(Command)\n", " Inputs: \n", " Primary: (0x35f5aa0) *\n", " _1: (0x35f0b90)\n", " Indexed Inputs: \n", " 0: Primary (0x35f5aa0)\n", " 1: _1 (0x35f0b90)\n", " Required Input Names: Primary\n", " NumberOfRequiredInputs: 1\n", " Outputs: \n", " Primary: (0x35ed070)\n", " Indexed Outputs: \n", " 0: Primary (0x35ed070)\n", " NumberOfRequiredOutputs: 1\n", " Number Of Threads: 32\n", " ReleaseDataFlag: Off\n", " ReleaseDataBeforeUpdateFlag: Off\n", " AbortGenerateData: Off\n", " Progress: 0\n", " Multithreader: \n", " RTTI typeinfo: itk::PoolMultiThreader\n", " Reference Count: 1\n", " Modified Time: 207\n", " Debug: Off\n", " Object Name: \n", " Observers: \n", " none\n", " DynamicMultiThreading: On\n", " CoordinateTolerance: 1e-06\n", " DirectionTolerance: 1e-06\n", " Maximum number of iterations: 3\n", " Convergence threshold: 0\n", " Number of tissue classes: 3\n", " Number of partial volume classes: 0\n", " Minimize memory usage: false\n", " Initialization strategy: K means clustering\n", " Posterior probability formulation: Socrates\n", " initial annealing temperature = 1\n", " annealing rate = 1\n", " minimum annealing temperature = 0.1\n", " MRF parameters\n", " MRF smoothing factor = 0.1\n", " MRF radius = [1, 1, 1]\n", " Use asynchronous updating of the labels.\n", " ICM parameters\n", " maximum ICM code = 13\n", " maximum number of ICM iterations = 1\n", " No outlier handling.\n", " Tissue class 1: proportion = 0.217436\n", " GaussianListSampleFunction (0x35f3e20)\n", " mean = [62.83238467660718], covariance = [898.21]\n", " Tissue class 2: proportion = 0.418785\n", " GaussianListSampleFunction (0x35f0ed0)\n", " mean = [138.786932061166], covariance = [535.752]\n", " Tissue class 3: proportion = 0.363935\n", " GaussianListSampleFunction (0x35f8390)\n", " mean = [220.9773010244717], covariance = [370.012]\n", "Elapsed time: 42.7614\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "/opt/ants-2.3.1//ImageMath 3 ANTS_Stripped_BrainExtractionSegmentation.nii.gz PadImage ANTS_Stripped_BrainExtractionSegmentation.nii.gz 10\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "/opt/ants-2.3.1//ImageMath 3 ANTS_Stripped_BrainExtractionPriorWarped.nii.gz PadImage ANTS_Stripped_BrainExtractionPriorWarped.nii.gz 10\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "/opt/ants-2.3.1//ThresholdImage 3 ANTS_Stripped_BrainExtractionSegmentation.nii.gz ANTS_Stripped_BrainExtractionWM.nii.gz 3 3 1 0\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "/opt/ants-2.3.1//ThresholdImage 3 ANTS_Stripped_BrainExtractionSegmentation.nii.gz ANTS_Stripped_BrainExtractionGM.nii.gz 2 2 1 0\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "/opt/ants-2.3.1//ThresholdImage 3 ANTS_Stripped_BrainExtractionSegmentation.nii.gz ANTS_Stripped_BrainExtractionCSF.nii.gz 1 1 1 0\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "/opt/ants-2.3.1//ImageMath 3 ANTS_Stripped_BrainExtractionWM.nii.gz GetLargestComponent ANTS_Stripped_BrainExtractionWM.nii.gz\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "/opt/ants-2.3.1//ImageMath 3 ANTS_Stripped_BrainExtractionGM.nii.gz GetLargestComponent ANTS_Stripped_BrainExtractionGM.nii.gz\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "/opt/ants-2.3.1//ImageMath 3 ANTS_Stripped_BrainExtractionTmp.nii.gz FillHoles ANTS_Stripped_BrainExtractionGM.nii.gz 2\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "/opt/ants-2.3.1//MultiplyImages 3 ANTS_Stripped_BrainExtractionGM.nii.gz ANTS_Stripped_BrainExtractionTmp.nii.gz ANTS_Stripped_BrainExtractionGM.nii.gz\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "/opt/ants-2.3.1//MultiplyImages 3 ANTS_Stripped_BrainExtractionWM.nii.gz 3 ANTS_Stripped_BrainExtractionWM.nii.gz\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "/opt/ants-2.3.1//ImageMath 3 ANTS_Stripped_BrainExtractionTmp.nii.gz ME ANTS_Stripped_BrainExtractionCSF.nii.gz 10\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "/opt/ants-2.3.1//ImageMath 3 ANTS_Stripped_BrainExtractionGM.nii.gz addtozero ANTS_Stripped_BrainExtractionGM.nii.gz ANTS_Stripped_BrainExtractionTmp.nii.gz\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "/opt/ants-2.3.1//MultiplyImages 3 ANTS_Stripped_BrainExtractionGM.nii.gz 2 ANTS_Stripped_BrainExtractionGM.nii.gz\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "/opt/ants-2.3.1//ImageMath 3 ANTS_Stripped_BrainExtractionSegmentation.nii.gz addtozero ANTS_Stripped_BrainExtractionWM.nii.gz ANTS_Stripped_BrainExtractionGM.nii.gz\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "/opt/ants-2.3.1//ThresholdImage 3 ANTS_Stripped_BrainExtractionSegmentation.nii.gz ANTS_Stripped_BrainExtractionMask.nii.gz 3 3 1 0\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "/opt/ants-2.3.1//ThresholdImage 3 ANTS_Stripped_BrainExtractionSegmentation.nii.gz ANTS_Stripped_BrainExtractionTmp.nii.gz 2 2 1 0\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "/opt/ants-2.3.1//ImageMath 3 ANTS_Stripped_BrainExtractionMask.nii.gz addtozero ANTS_Stripped_BrainExtractionMask.nii.gz ANTS_Stripped_BrainExtractionTmp.nii.gz\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "/opt/ants-2.3.1//ImageMath 3 ANTS_Stripped_BrainExtractionMask.nii.gz ME ANTS_Stripped_BrainExtractionMask.nii.gz 2\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "/opt/ants-2.3.1//ImageMath 3 ANTS_Stripped_BrainExtractionMask.nii.gz GetLargestComponent ANTS_Stripped_BrainExtractionMask.nii.gz\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "/opt/ants-2.3.1//ImageMath 3 ANTS_Stripped_BrainExtractionMask.nii.gz MD ANTS_Stripped_BrainExtractionMask.nii.gz 4\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "/opt/ants-2.3.1//ImageMath 3 ANTS_Stripped_BrainExtractionMask.nii.gz FillHoles ANTS_Stripped_BrainExtractionMask.nii.gz 2\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "/opt/ants-2.3.1//ImageMath 3 ANTS_Stripped_BrainExtractionMask.nii.gz addtozero ANTS_Stripped_BrainExtractionMask.nii.gz ANTS_Stripped_BrainExtractionPriorWarped.nii.gz\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "/opt/ants-2.3.1//ImageMath 3 ANTS_Stripped_BrainExtractionMask.nii.gz MD ANTS_Stripped_BrainExtractionMask.nii.gz 5\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "/opt/ants-2.3.1//ImageMath 3 ANTS_Stripped_BrainExtractionMask.nii.gz ME ANTS_Stripped_BrainExtractionMask.nii.gz 5\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "/opt/ants-2.3.1//ImageMath 3 ANTS_Stripped_BrainExtractionSegmentation.nii.gz PadImage ANTS_Stripped_BrainExtractionSegmentation.nii.gz -10\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "/opt/ants-2.3.1//ImageMath 3 ANTS_Stripped_BrainExtractionMask.nii.gz PadImage ANTS_Stripped_BrainExtractionMask.nii.gz -10\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "/opt/ants-2.3.1//ImageMath 3 ANTS_Stripped_BrainExtractionWM.nii.gz PadImage ANTS_Stripped_BrainExtractionWM.nii.gz -10\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "/opt/ants-2.3.1//ImageMath 3 ANTS_Stripped_BrainExtractionGM.nii.gz PadImage ANTS_Stripped_BrainExtractionGM.nii.gz -10\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "/opt/ants-2.3.1//ImageMath 3 ANTS_Stripped_BrainExtractionCSF.nii.gz PadImage ANTS_Stripped_BrainExtractionCSF.nii.gz -10\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "/opt/ants-2.3.1//ImageMath 3 ANTS_Stripped_BrainExtractionPriorWarped.nii.gz PadImage ANTS_Stripped_BrainExtractionPriorWarped.nii.gz -10\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "/opt/ants-2.3.1//MultiplyImages 3 ANTS_Stripped_N4Corrected0.nii.gz ANTS_Stripped_BrainExtractionMask.nii.gz ANTS_Stripped_BrainExtractionBrain.nii.gz\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "\n", "--------------------------------------------------------------------------------------\n", " Done with brain extraction: 0h 13m 18s\n", "--------------------------------------------------------------------------------------\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "rm ANTS_Stripped_BrainExtractionPriorWarped.nii.gz\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "rm ANTS_Stripped_BrainExtractionPrior1Warp.nii.gz\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "rm ANTS_Stripped_BrainExtractionPrior1InverseWarp.nii.gz\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "rm ANTS_Stripped_BrainExtractionTmp.nii.gz\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "rm ANTS_Stripped_BrainExtractionGM.nii.gz\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "rm ANTS_Stripped_BrainExtractionCSF.nii.gz\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "rm ANTS_Stripped_BrainExtractionSegmentation.nii.gz\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "rm ANTS_Stripped_BrainExtractionInitialAffine.mat\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "rm ANTS_Stripped_BrainExtractionInitialAffineMoving.nii.gz\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "rm ANTS_Stripped_BrainExtractionInitialAffineFixed.nii.gz\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "rm ANTS_Stripped_BrainExtractionLaplacian.nii.gz\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "rm ANTS_Stripped_BrainExtractionTemplateLaplacian.nii.gz\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "rm ANTS_Stripped_BrainExtractionWM.nii.gz\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "rm ANTS_Stripped_N4Truncated0.nii.gz\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n", "BEGIN >>>>>>>>>>>>>>>>>>>>\n", "rm ANTS_Stripped_N4Corrected0.nii.gz\n", "END <<<<<<<<<<<<<<<<<<<<\n", "\n", "\n" ] } ], "source": [ "! antsBrainExtraction.sh -d 3 -a $input_image -e $brain_template -m $brain_prior -o ANTS_Stripped_" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "The option ```-d 3``` means that it is a three-dimensional image; ```-a``` indicates the anatomical image to be stripped; and ```-e``` is used to supply a an anatomical template (with skull) and ```-m``` to provide a brain probability mask for skull-stripping , and ```-o``` is the label (prefix) for the output." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### 2. AFNI\n", "Next, we will use AFNI's 3dSkullStrip for brain extraction" ] }, { "cell_type": "code", "execution_count": 13, "metadata": { "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n", "Usage: A program to extract the brain from surrounding.\n", " tissue from MRI T1-weighted images. \n", " The simplest command would be:\n", " 3dSkullStrip <-input DSET>\n", "\n", " Also consider the script @SSwarper, which combines the use of\n", " 3dSkullStrip and nonlinear warping to an MNI template to produce\n", " a skull-stripped dataset in MNI space, plus the nonlinear warp\n", " that can used to transform other datasets from the same subject\n", " (e.g., EPI) to MNI space. (This script only applies to human brain\n", " images.)\n", "\n", " The fully automated process consists of three steps:\n", " 1- Preprocessing of volume to remove gross spatial image \n", " non-uniformity artifacts and reposition the brain in\n", " a reasonable manner for convenience.\n", " ** Note that in many cases, using 3dUnifize before **\n", " ** using 3dSkullStrip will give better results. **\n", " 2- Expand a spherical surface iteratively until it envelopes\n", " the brain. This is a modified version of the BET algorithm:\n", " Fast robust automated brain extraction, \n", " by Stephen M. Smith, HBM 2002 v 17:3 pp 143-155\n", " Modifications include the use of:\n", " . outer brain surface\n", " . expansion driven by data inside and outside the surface\n", " . avoidance of eyes and ventricles\n", " . a set of operations to avoid the clipping of certain brain\n", " areas and reduce leakage into the skull in heavily shaded\n", " data\n", " . two additional processing stages to ensure convergence and\n", " reduction of clipped areas.\n", " . use of 3d edge detection, see Deriche and Monga references\n", " in 3dedge3 -help.\n", " 3- The creation of various masks and surfaces modeling brain\n", " and portions of the skull\n", "\n", " Common examples of usage:\n", " -------------------------\n", " o 3dSkullStrip -input VOL -prefix VOL_PREFIX\n", " Vanilla mode, should work for most datasets.\n", " o 3dSkullStrip -input VOL -prefix VOL_PREFIX -push_to_edge\n", " Adds an aggressive push to brain edges. Use this option\n", " when the chunks of gray matter are not included. This option\n", " might cause the mask to leak into non-brain areas.\n", " o 3dSkullStrip -input VOL -surface_coil -prefix VOL_PREFIX -monkey\n", " Vanilla mode, for use with monkey data.\n", " o 3dSkullStrip -input VOL -prefix VOL_PREFIX -ld 30\n", " Use a denser mesh, in the cases where you have lots of \n", " csf between gyri. Also helps when some of the brain is clipped\n", " close to regions of high curvature.\n", "\n", " Tips:\n", " -----\n", " I ran the program with the default parameters on 200+ datasets.\n", " The results were quite good in all but a couple of instances, here\n", " are some tips on fixing trouble spots:\n", "\n", " Clipping in frontal areas, close to the eye balls:\n", " + Try -push_to_edge option first.\n", " Can also try -no_avoid_eyes option.\n", " Clipping in general:\n", " + Try -push_to_edge option first.\n", " Can also use lower -shrink_fac, start with 0.5 then 0.4\n", " Problems down below:\n", " + Piece of cerebellum missing, reduce -shrink_fac_bot_lim \n", " from default value.\n", " + Leakage in lower areas, increase -shrink_fac_bot_lim \n", " from default value.\n", " Some lobules are not included:\n", " + Use a denser mesh. Start with -ld 30. If that still fails,\n", " try even higher density (like -ld 50) and increase iterations \n", " (say to -niter 750). \n", " Expect the program to take much longer in that case.\n", " + Instead of using denser meshes, you could try blurring the data \n", " before skull stripping. Something like -blur_fwhm 2 did\n", " wonders for some of my data with the default options of 3dSkullStrip\n", " Blurring is a lot faster than increasing mesh density.\n", " + Use also a smaller -shrink_fac is you have lots of CSF between\n", " gyri.\n", " Massive chunks missing:\n", " + If brain has very large ventricles and lots of CSF between gyri,\n", " the ventricles will keep attracting the surface inwards. \n", " This often happens with older brains. In such \n", " cases, use the -visual option to see what is happening.\n", " For example, the options below did the trick in various\n", " instances. \n", " -blur_fwhm 2 -use_skull \n", " or for more stubborn cases increase csf avoidance with this cocktail\n", " -blur_fwhm 2 -use_skull -avoid_vent -avoid_vent -init_radius 75 \n", " + Too much neck in the volume might throw off the initialization\n", " step. You can fix this by clipping tissue below the brain with \n", " @clip_volume -below ZZZ -input INPUT \n", " where ZZZ is a Z coordinate somewhere below the brain.\n", "\n", " Large regions outside brain included:\n", " + Usually because noise level is high. Try @NoisySkullStrip.\n", "\n", " Make sure that brain orientation is correct. This means the image in \n", " AFNI's axial slice viewer should be close to the brain's axial plane.\n", " The same goes for the other planes. Otherwise, the program might do a lousy\n", " job removing the skull.\n", "\n", " Eye Candy Mode: \n", " ---------------\n", " You can run 3dSkullStrip and have it send successive iterations\n", " to SUMA and AFNI. This is very helpful in following the\n", " progression of the algorithm and determining the source\n", " of trouble, if any.\n", " Example:\n", " afni -niml -yesplugouts &\n", " suma -niml &\n", " 3dSkullStrip -input Anat+orig -o_ply anat_brain -visual\n", "\n", " Help section for the intrepid:\n", " ------------------------------\n", " 3dSkullStrip < -input VOL >\n", " [< -o_TYPE PREFIX >] [< -prefix VOL_PREFIX >] \n", " [< -spatnorm >] [< -no_spatnorm >] [< -write_spatnorm >]\n", " [< -niter N_ITER >] [< -ld LD >] \n", " [< -shrink_fac SF >] [< -var_shrink_fac >] \n", " [< -no_var_shrink_fac >] [< -shrink_fac_bot_lim SFBL >]\n", " [< -pushout >] [< -no_pushout >] [< -exp_frac FRAC]\n", " [< -touchup >] [< -no_touchup >]\n", " [< -fill_hole R >] [< -NN_smooth NN_SM >]\n", " [< -smooth_final SM >] [< -avoid_vent >] [< -no_avoid_vent >]\n", " [< -use_skull >] [< -no_use_skull >] \n", " [< -avoid_eyes >] [< -no_avoid_eyes >] \n", " [< -use_edge >] [< -no_use_edge >] \n", " [< -push_to_edge >] [<-no_push_to_edge>]\n", " [< -perc_int PERC_INT >] \n", " [< -max_inter_iter MII >] [-mask_vol | -orig_vol | -norm_vol]\n", " [< -debug DBG >] [< -node_debug NODE_DBG >]\n", " [< -demo_pause >]\n", " [< -monkey >] [< -marmoset >] [<-rat>]\n", "\n", " NOTE: Please report bugs and strange failures\n", " to saadz@mail.nih.gov\n", "\n", " Mandatory parameters:\n", " -input VOL: Input AFNI (or AFNI readable) volume.\n", " \n", "\n", " Optional Parameters:\n", " -monkey: the brain of a monkey.\n", " -marmoset: the brain of a marmoset. \n", " this one was tested on one dataset\n", " and may not work with non default\n", " options. Check your results!\n", " -rat: the brain of a rat.\n", " By default, no_touchup is used with the rat.\n", " -surface_coil: Data acquired with a surface coil.\n", " -o_TYPE PREFIX: prefix of output surface.\n", " where TYPE specifies the format of the surface\n", " and PREFIX is, well, the prefix.\n", " TYPE is one of: fs, 1d (or vec), sf, ply.\n", " More on that below.\n", " -skulls: Output surface models of the skull.\n", " -4Tom: The output surfaces are named based\n", " on PREFIX following -o_TYPE option below.\n", " -prefix VOL_PREFIX: prefix of output volume.\n", " If not specified, the prefix is the same\n", " as the one used with -o_TYPE.\n", " The output volume is skull stripped version\n", " of the input volume. In the earlier version\n", " of the program, a mask volume was written out.\n", " You can still get that mask volume instead of the\n", " skull-stripped volume with the option -mask_vol . \n", " NOTE: In the default setting, the output volume does not \n", " have values identical to those in the input. \n", " In particular, the range might be larger \n", " and some low-intensity values are set to 0.\n", " If you insist on having the same range of values as in\n", " the input, then either use option -orig_vol, or run:\n", " 3dcalc -nscale -a VOL+VIEW -b VOL_PREFIX+VIEW \\\n", " -expr 'a*step(b)' -prefix VOL_SAME_RANGE\n", " With the command above, you can preserve the range\n", " of values of the input but some low-intensity voxels would\n", " still be masked. If you want to preserve them, then use\n", " -mask_vol in the 3dSkullStrip command that would produce \n", " VOL_MASK_PREFIX+VIEW. Then run 3dcalc masking with voxels\n", " inside the brain surface envelope:\n", " 3dcalc -nscale -a VOL+VIEW -b VOL_MASK_PREFIX+VIEW \\\n", " -expr 'a*step(b-3.01)' -prefix VOL_SAME_RANGE_KEEP_LOW\n", " -norm_vol: Output a masked and somewhat intensity normalized and \n", " thresholded version of the input. This is the default,\n", " and you can use -orig_vol to override it.\n", " -orig_vol: Output a masked version of the input AND do not modify\n", " the values inside the brain as -norm_vol would.\n", " -mask_vol: Output a mask volume instead of a skull-stripped\n", " volume.\n", " The mask volume contains:\n", " 0: Voxel outside surface\n", " 1: Voxel just outside the surface. This means the voxel\n", " center is outside the surface but inside the \n", " bounding box of a triangle in the mesh. \n", " 2: Voxel intersects the surface (a triangle), but center\n", " lies outside.\n", " 3: Voxel contains a surface node.\n", " 4: Voxel intersects the surface (a triangle), center lies\n", " inside surface. \n", " 5: Voxel just inside the surface. This means the voxel\n", " center is inside the surface and inside the \n", " bounding box of a triangle in the mesh. \n", " 6: Voxel inside the surface. \n", " -spat_norm: (Default) Perform spatial normalization first.\n", " This is a necessary step unless the volume has\n", " been 'spatnormed' already.\n", " -no_spatnorm: Do not perform spatial normalization.\n", " Use this option only when the volume \n", " has been run through the 'spatnorm' process\n", " -spatnorm_dxyz DXYZ: Use DXY for the spatial resolution of the\n", " spatially normalized volume. The default \n", " is the lowest of all three dimensions.\n", " For human brains, use DXYZ of 1.0, for\n", " primate brain, use the default setting.\n", " -write_spatnorm: Write the 'spatnormed' volume to disk.\n", " -niter N_ITER: Number of iterations. Default is 250\n", " For denser meshes, you need more iterations\n", " N_ITER of 750 works for LD of 50.\n", " -ld LD: Parameter to control the density of the surface.\n", " Default is 20 if -no_use_edge is used,\n", " 30 with -use_edge. See CreateIcosahedron -help\n", " for details on this option.\n", " -shrink_fac SF: Parameter controlling the brain vs non-brain\n", " intensity threshold (tb). Default is 0.6.\n", " tb = (Imax - t2) SF + t2 \n", " where t2 is the 2 percentile value and Imax is the local\n", " maximum, limited to the median intensity value.\n", " For more information on tb, t2, etc. read the BET paper\n", " mentioned above. Note that in 3dSkullStrip, SF can vary across \n", " iterations and might be automatically clipped in certain areas.\n", " SF can vary between 0 and 1.\n", " 0: Intensities < median inensity are considered non-brain\n", " 1: Intensities < t2 are considered non-brain\n", " -var_shrink_fac: Vary the shrink factor with the number of\n", " iterations. This reduces the likelihood of a surface\n", " getting stuck on large pools of CSF before reaching\n", " the outer surface of the brain. (Default)\n", " -no_var_shrink_fac: Do not use var_shrink_fac.\n", " -shrink_fac_bot_lim SFBL: Do not allow the varying SF to go\n", " below SFBL . Default 0.65, 0.4 when edge detection is used. \n", " This option helps reduce potential for leakage below \n", " the cerebellum.\n", " In certain cases where you have severe non-uniformity resulting\n", " in low signal towards the bottom of the brain, you will need to\n", " reduce this parameter.\n", " -pushout: Consider values above each node in addition to values\n", " below the node when deciding on expansion. (Default)\n", " -no_pushout: Do not use -pushout.\n", " -exp_frac FRAC: Speed of expansion (see BET paper). Default is 0.1.\n", " -touchup: Perform touchup operations at end to include\n", " areas not covered by surface expansion. \n", " Use -touchup -touchup for aggressive makeup.\n", " (Default is -touchup)\n", " -no_touchup: Do not use -touchup\n", " -fill_hole R: Fill small holes that can result from small surface\n", " intersections caused by the touchup operation.\n", " R is the maximum number of pixels on the side of a hole\n", " that can be filled. Big holes are not filled.\n", " If you use -touchup, the default R is 10. Otherwise \n", " the default is 0.\n", " This is a less than elegant solution to the small\n", " intersections which are usually eliminated\n", " automatically. \n", " -NN_smooth NN_SM: Perform Nearest Neighbor coordinate interpolation\n", " every few iterations. Default is 72\n", " -smooth_final SM: Perform final surface smoothing after all iterations.\n", " Default is 20 smoothing iterations.\n", " Smoothing is done using Taubin's method, \n", " see SurfSmooth -help for detail.\n", " -avoid_vent: avoid ventricles. Default.\n", " Use this option twice to make the avoidance more\n", " aggressive. That is at times needed with old brains.\n", " -no_avoid_vent: Do not use -avoid_vent.\n", " -init_radius RAD: Use RAD for the initial sphere radius.\n", " For the automatic setting, there is an\n", " upper limit of 100mm for humans.\n", " For older brains with lots of CSF, you\n", " might benefit from forcing the radius \n", " to something like 75mm\n", " -avoid_eyes: avoid eyes. Default\n", " -no_avoid_eyes: Do not use -avoid_eyes.\n", " -use_edge: Use edge detection to reduce leakage into meninges and eyes.\n", " Default.\n", " -no_use_edge: Do no use edges.\n", " -push_to_edge: Perform aggressive push to edge at the end.\n", " This option might cause leakage.\n", " -no_push_to_edge: (Default).\n", " -use_skull: Use outer skull to limit expansion of surface into\n", " the skull due to very strong shading artifacts.\n", " This option is buggy at the moment, use it only \n", " if you have leakage into skull.\n", " -no_use_skull: Do not use -use_skull (Default).\n", " -send_no_skull: Do not send the skull surface to SUMA if you are\n", " using -talk_suma\n", " -perc_int PERC_INT: Percentage of segments allowed to intersect\n", " surface. Ideally this should be 0 (Default). \n", " However, few surfaces might have small stubborn\n", " intersections that produce a few holes.\n", " PERC_INT should be a small number, typically\n", " between 0 and 0.1. A -1 means do not do\n", " any testing for intersection.\n", " -max_inter_iter N_II: Number of iteration to remove intersection\n", " problems. With each iteration, the program\n", " automatically increases the amount of smoothing\n", " to get rid of intersections. Default is 4\n", " -blur_fwhm FWHM: Blur dset after spatial normalization.\n", " Recommended when you have lots of CSF in brain\n", " and when you have protruding gyri (finger like)\n", " Recommended value is 2..4. \n", " -interactive: Make the program stop at various stages in the \n", " segmentation process for a prompt from the user\n", " to continue or skip that stage of processing.\n", " This option is best used in conjunction with options\n", " -talk_suma and -feed_afni\n", " -demo_pause: Pause at various step in the process to facilitate\n", " interactive demo while 3dSkullStrip is communicating\n", " with AFNI and SUMA. See 'Eye Candy' mode below and\n", " -talk_suma option. \n", " -fac FAC: Multiply input dataset by FAC if range of values is too\n", " small.\n", "\n", " Specifying output surfaces using -o or -o_TYPE options: \n", " -o_TYPE outSurf specifies the output surface, \n", " TYPE is one of the following:\n", " fs: FreeSurfer ascii surface. \n", " fsp: FeeSurfer ascii patch surface. \n", " In addition to outSurf, you need to specify\n", " the name of the parent surface for the patch.\n", " using the -ipar_TYPE option.\n", " This option is only for ConvertSurface \n", " sf: SureFit surface. \n", " For most programs, you are expected to specify prefix:\n", " i.e. -o_sf brain. In some programs, you are allowed to \n", " specify both .coord and .topo file names: \n", " i.e. -o_sf XYZ.coord TRI.topo\n", " The program will determine your choice by examining \n", " the first character of the second parameter following\n", " -o_sf. If that character is a '-' then you have supplied\n", " a prefix and the program will generate the coord and topo names.\n", " vec (or 1D): Simple ascii matrix format. \n", " For most programs, you are expected to specify prefix:\n", " i.e. -o_1D brain. In some programs, you are allowed to \n", " specify both coord and topo file names: \n", " i.e. -o_1D brain.1D.coord brain.1D.topo\n", " coord contains 3 floats per line, representing \n", " X Y Z vertex coordinates.\n", " topo contains 3 ints per line, representing \n", " v1 v2 v3 triangle vertices.\n", " ply: PLY format, ascii or binary.\n", " stl: STL format, ascii or binary (see also STL under option -i_TYPE).\n", " byu: BYU format, ascii or binary.\n", " mni: MNI obj format, ascii only.\n", " gii: GIFTI format, ascii.\n", " You can also enforce the encoding of data arrays\n", " by using gii_asc, gii_b64, or gii_b64gz for \n", " ASCII, Base64, or Base64 Gzipped. \n", " If AFNI_NIML_TEXT_DATA environment variable is set to YES, the\n", " the default encoding is ASCII, otherwise it is Base64.\n", " obj: No support for writing OBJ format exists yet.\n", " Note that if the surface filename has the proper extension, \n", " it is enough to use the -o option and let the programs guess\n", " the type from the extension.\n", "\n", " SUMA communication options:\n", " -talk_suma: Send progress with each iteration to SUMA.\n", " -refresh_rate rps: Maximum number of updates to SUMA per second.\n", " The default is the maximum speed.\n", " -send_kth kth: Send the kth element to SUMA (default is 1).\n", " This allows you to cut down on the number of elements\n", " being sent to SUMA.\n", " -sh : Name (or IP address) of the computer running SUMA.\n", " This parameter is optional, the default is 127.0.0.1 \n", " -ni_text: Use NI_TEXT_MODE for data transmission.\n", " -ni_binary: Use NI_BINARY_MODE for data transmission.\n", " (default is ni_binary).\n", " -feed_afni: Send updates to AFNI via SUMA's talk.\n", " -np PORT_OFFSET: Provide a port offset to allow multiple instances of\n", " AFNI <--> SUMA, AFNI <--> 3dGroupIncorr, or any other\n", " programs that communicate together to operate on the same\n", " machine. \n", " All ports are assigned numbers relative to PORT_OFFSET.\n", " The same PORT_OFFSET value must be used on all programs\n", " that are to talk together. PORT_OFFSET is an integer in\n", " the inclusive range [1025 to 65500]. \n", " When you want to use multiple instances of communicating programs, \n", " be sure the PORT_OFFSETS you use differ by about 50 or you may\n", " still have port conflicts. A BETTER approach is to use -npb below.\n", " -npq PORT_OFFSET: Like -np, but more quiet in the face of adversity.\n", " -npb PORT_OFFSET_BLOC: Similar to -np, except it is easier to use.\n", " PORT_OFFSET_BLOC is an integer between 0 and\n", " MAX_BLOC. MAX_BLOC is around 4000 for now, but\n", " it might decrease as we use up more ports in AFNI.\n", " You should be safe for the next 10 years if you \n", " stay under 2000.\n", " Using this function reduces your chances of causing\n", " port conflicts.\n", "\n", " See also afni and suma options: -list_ports and -port_number for \n", " information about port number assignments.\n", "\n", " You can also provide a port offset with the environment variable\n", " AFNI_PORT_OFFSET. Using -np overrides AFNI_PORT_OFFSET.\n", "\n", " -max_port_bloc: Print the current value of MAX_BLOC and exit.\n", " Remember this value can get smaller with future releases.\n", " Stay under 2000.\n", " -max_port_bloc_quiet: Spit MAX_BLOC value only and exit.\n", " -num_assigned_ports: Print the number of assigned ports used by AFNI \n", " then quit.\n", " -num_assigned_ports_quiet: Do it quietly.\n", "\n", " Port Handling Examples:\n", " -----------------------\n", " Say you want to run three instances of AFNI <--> SUMA.\n", " For the first you just do: \n", " suma -niml -spec ... -sv ... &\n", " afni -niml &\n", " Then for the second instance pick an offset bloc, say 1 and run\n", " suma -niml -npb 1 -spec ... -sv ... &\n", " afni -niml -npb 1 &\n", " And for yet another instance:\n", " suma -niml -npb 2 -spec ... -sv ... &\n", " afni -niml -npb 2 &\n", " etc.\n", "\n", " Since you can launch many instances of communicating programs now,\n", " you need to know wich SUMA window, say, is talking to which AFNI.\n", " To sort this out, the titlebars now show the number of the bloc \n", " of ports they are using. When the bloc is set either via \n", " environment variables AFNI_PORT_OFFSET or AFNI_PORT_BLOC, or \n", " with one of the -np* options, window title bars change from \n", " [A] to [A#] with # being the resultant bloc number.\n", " In the examples above, both AFNI and SUMA windows will show [A2]\n", " when -npb is 2.\n", "\n", "\n", "\n", " -visual: Equivalent to using -talk_suma -feed_afni -send_kth 5\n", "\n", " -debug DBG: debug levels of 0 (default), 1, 2, 3.\n", " This is no Rick Reynolds debug, which is oft nicer\n", " than the results, but it will do.\n", " -node_debug NODE_DBG: Output lots of parameters for node\n", " NODE_DBG for each iteration.\n", " The next 3 options are for specifying surface coordinates\n", " to keep the program from having to recompute them.\n", " The options are only useful for saving time during debugging.\n", " -brain_contour_xyz_file BRAIN_CONTOUR_XYZ.1D\n", " -brain_hull_xyz_file BRAIN_HULL_XYZ.1D\n", " -skull_outer_xyz_file SKULL_OUTER_XYZ.1D\n", " -help: The help you need\n", "\n", " [-novolreg]: Ignore any Rotate, Volreg, Tagalign, \n", " or WarpDrive transformations present in \n", " the Surface Volume.\n", " [-noxform]: Same as -novolreg\n", " [-setenv \"'ENVname=ENVvalue'\"]: Set environment variable ENVname\n", " to be ENVvalue. Quotes are necessary.\n", " Example: suma -setenv \"'SUMA_BackgroundColor = 1 0 1'\"\n", " See also options -update_env, -environment, etc\n", " in the output of 'suma -help'\n", " Common Debugging Options:\n", " [-trace]: Turns on In/Out debug and Memory tracing.\n", " For speeding up the tracing log, I recommend \n", " you redirect stdout to a file when using this option.\n", " For example, if you were running suma you would use:\n", " suma -spec lh.spec -sv ... > TraceFile\n", " This option replaces the old -iodbg and -memdbg.\n", " [-TRACE]: Turns on extreme tracing.\n", " [-nomall]: Turn off memory tracing.\n", " [-yesmall]: Turn on memory tracing (default).\n", " NOTE: For programs that output results to stdout\n", " (that is to your shell/screen), the debugging info\n", " might get mixed up with your results.\n", "\n", "\n", "Global Options (available to all AFNI/SUMA programs)\n", " -h: Mini help, at time, same as -help in many cases.\n", " -help: The entire help output\n", " -HELP: Extreme help, same as -help in majority of cases.\n", " -h_view: Open help in text editor. AFNI will try to find a GUI editor\n", " -hview : on your machine. You can control which it should use by\n", " setting environment variable AFNI_GUI_EDITOR.\n", " -h_web: Open help in web browser. AFNI will try to find a browser.\n", " -hweb : on your machine. You can control which it should use by\n", " setting environment variable AFNI_GUI_EDITOR. \n", " -h_find WORD: Look for lines in this programs's -help output that match\n", " (approximately) WORD.\n", " -h_raw: Help string unedited\n", " -h_spx: Help string in sphinx loveliness, but do not try to autoformat\n", " -h_aspx: Help string in sphinx with autoformatting of options, etc.\n", " -all_opts: Try to identify all options for the program from the\n", " output of its -help option. Some options might be missed\n", " and others misidentified. Use this output for hints only.\n", " \n", "\n", "\n", "Compile Date:\n", " Apr 9 2024\n", "\n", " Ziad S. Saad SSCC/NIMH/NIH saadz@mail.nih.gov \n" ] } ], "source": [ "! 3dSkullStrip -help" ] }, { "cell_type": "code", "execution_count": 14, "metadata": { "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "3dSkullStrip: Pushing to Edge ...\n", "The intensity in the output dataset is a modified version\n", "of the intensity in the input volume.\n", "To obtain a masked version of the input with identical values inside\n", "the brain, you can either use 3dSkullStrip's -orig_vol option\n", "or run the following command:\n", " 3dcalc -a ds000102/sub-08/anat/sub-08_T1w.nii.gz -b ./AFNI_ss.nii.gz+orig -expr 'a*step(b)' \\\n", " -prefix ./AFNI_ss.nii.gz_orig_vol\n", "to generate a new masked version of the input.\n" ] } ], "source": [ "! 3dSkullStrip -input $input_image -prefix AFNI_ss.nii.gz -push_to_edge" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "From [AFNI's documentation](https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dSkullStrip.html):\n", "\n", "```-push_to_edge```: Adds an aggressive push to brain edges. Use this option when the chunks of gray matter are not included. This option might cause the mask to leak into non-brain areas." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### 3. FreeSurfer\n", "FreeSurfer's SynthStrip is a skull-stripping tool that extracts brain voxels from a landscape of image types, ranging across imaging modalities, resolutions, and subject populations. It leverages a deep learning strategy to synthesize arbitrary training images from segmentation maps, yielding a robust model agnostic to acquisition specifics.\n", "\n" ] }, { "cell_type": "code", "execution_count": 15, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "usage: mri_synthstrip [-h] -i file [-o file] [-m file] [-g] [-b BORDER]\n", " [--no-csf] [--model file]\n", "\n", "Robust, universal skull-stripping for brain images of any type. If you use\n", "SynthStrip in your analysis, please cite: SynthStrip: Skull-Stripping for Any\n", "Brain Image. A Hoopes, JS Mora, AV Dalca, B Fischl, M Hoffmann. NeuroImage 206\n", "(2022), 119474. https://doi.org/10.1016/j.neuroimage.2022.119474\n", "\n", "optional arguments:\n", " -h, --help show this help message and exit\n", " -i file, --image file\n", " Input image to skullstrip.\n", " -o file, --out file Save stripped image to path.\n", " -m file, --mask file Save binary brain mask to path.\n", " -g, --gpu Use the GPU.\n", " -b BORDER, --border BORDER\n", " Mask border threshold in mm. Default is 1.\n", " --no-csf Exclude CSF from brain border.\n", " --model file Alternative model weights.\n" ] } ], "source": [ "! mri_synthstrip --help" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Next, you can run SynthStrip using the following syntax. In this command, \"synth_stripped.nii.gz\" will be the skull-stripped version of the input image \"sub-08_T1w.nii.gz.\" Use the ```-m``` flag to save a binary brain mask:" ] }, { "cell_type": "code", "execution_count": 16, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Configuring model on the CPU\n", "Running SynthStrip model version 1\n", "Input image read from: ds000102/sub-08/anat/sub-08_T1w.nii.gz\n", "Masked image saved to: synth_stripped.nii.gz\n", "Binary brain mask saved to: synth_mask.nii.gz\n", "If you use SynthStrip in your analysis, please cite:\n", "----------------------------------------------------\n", "SynthStrip: Skull-Stripping for Any Brain Image.\n", "A Hoopes, JS Mora, AV Dalca, B Fischl, M Hoffmann.\n", "NeuroImage 206 (2022), 119474.\n" ] } ], "source": [ "! mri_synthstrip -i $input_image -o synth_stripped.nii.gz -m synth_mask.nii.gz" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### 4. FSL\n", "Another option for brain extraction is FSL’s BET (Brain Extraction Tool):" ] }, { "cell_type": "code", "execution_count": 17, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n", "Usage: bet [options]\n", "\n", "Main bet2 options:\n", " -o generate brain surface outline overlaid onto original image\n", " -m generate binary brain mask\n", " -s generate approximate skull image\n", " -n don't generate segmented brain image output\n", " -f fractional intensity threshold (0->1); default=0.5; smaller values give larger brain outline estimates\n", " -g vertical gradient in fractional intensity threshold (-1->1); default=0; positive values give larger brain outline at bottom, smaller at top\n", " -r head radius (mm not voxels); initial surface sphere is set to half of this\n", " -c centre-of-gravity (voxels not mm) of initial mesh surface.\n", " -t apply thresholding to segmented brain image and mask\n", " -e generates brain surface as mesh in .vtk format\n", "\n", "Variations on default bet2 functionality (mutually exclusive options):\n", " (default) just run bet2\n", " -R robust brain centre estimation (iterates BET several times)\n", " -S eye & optic nerve cleanup (can be useful in SIENA - disables -o option)\n", " -B bias field & neck cleanup (can be useful in SIENA)\n", " -Z improve BET if FOV is very small in Z (by temporarily padding end slices)\n", " -F apply to 4D FMRI data (uses -f 0.3 and dilates brain mask slightly)\n", " -A run bet2 and then betsurf to get additional skull and scalp surfaces (includes registrations)\n", " -A2 as with -A, when also feeding in non-brain-extracted T2 (includes registrations)\n", "\n", "Miscellaneous options:\n", " -v verbose (switch on diagnostic messages)\n", " -h display this help, then exits\n", " -d debug (don't delete temporary intermediate images)\n", "\n" ] } ], "source": [ "! bet" ] }, { "cell_type": "code", "execution_count": 18, "metadata": {}, "outputs": [], "source": [ "! bet $input_image anat_bet.nii.gz -m " ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Results\n", "Now we will compare the skull-stripped results with the original T1 image to assess the effectiveness of the brain extraction process." ] }, { "cell_type": "code", "execution_count": 19, "metadata": {}, "outputs": [ { "data": { "text/markdown": [ "### T1 image" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "b40c3fc3220a42c0b346beea1e7c0919", "version_major": 2, "version_minor": 0 }, "text/plain": [ "AnyNiivue()" ] }, "execution_count": 19, "metadata": {}, "output_type": "execute_result" } ], "source": [ "from ipyniivue import AnyNiivue\n", "from IPython.display import display, Markdown\n", "\n", "display(Markdown(\"### T1 image\"))\n", "\n", "nv_T1 = AnyNiivue()\n", "nv_T1.load_volumes([{\"path\": f\"{input_image}\"}])\n", "nv_T1" ] }, { "cell_type": "code", "execution_count": 20, "metadata": {}, "outputs": [ { "data": { "text/markdown": [ "### ANTs BrainExtraction" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "5445103eb09f41648387ccaae3650fd6", "version_major": 2, "version_minor": 0 }, "text/plain": [ "AnyNiivue()" ] }, "execution_count": 20, "metadata": {}, "output_type": "execute_result" } ], "source": [ "display(Markdown(\"### ANTs BrainExtraction\"))\n", "\n", "nv_ANTS = AnyNiivue()\n", "nv_ANTS.load_volumes([{\"path\": \"ANTS_Stripped_BrainExtractionBrain.nii.gz\"}])\n", "nv_ANTS " ] }, { "cell_type": "code", "execution_count": 21, "metadata": {}, "outputs": [ { "data": { "text/markdown": [ "### AFNI 3dSkullStrip" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "b47ee1980bb14c2a80ab7b0d893ef7be", "version_major": 2, "version_minor": 0 }, "text/plain": [ "AnyNiivue()" ] }, "execution_count": 21, "metadata": {}, "output_type": "execute_result" } ], "source": [ "display(Markdown(\"### AFNI 3dSkullStrip\"))\n", "\n", "nv_AFNI = AnyNiivue()\n", "nv_AFNI.load_volumes([{\"path\": \"AFNI_ss.nii.gz\"}])\n", "nv_AFNI" ] }, { "cell_type": "code", "execution_count": 22, "metadata": {}, "outputs": [ { "data": { "text/markdown": [ "### FreeSurfer SynthStrip" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "57050ef0ff874db9bfffab1d3f43cf6b", "version_major": 2, "version_minor": 0 }, "text/plain": [ "AnyNiivue()" ] }, "execution_count": 22, "metadata": {}, "output_type": "execute_result" } ], "source": [ "display(Markdown(\"### FreeSurfer SynthStrip\"))\n", "\n", "nv_FreeSurfer = AnyNiivue()\n", "nv_FreeSurfer.load_volumes([{\"path\": \"synth_stripped.nii.gz\"}])\n", "nv_FreeSurfer" ] }, { "cell_type": "code", "execution_count": 23, "metadata": {}, "outputs": [ { "data": { "text/markdown": [ "### FSL BET" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "90eff8a58b93440b9e7990d1c4f9afde", "version_major": 2, "version_minor": 0 }, "text/plain": [ "AnyNiivue()" ] }, "execution_count": 23, "metadata": {}, "output_type": "execute_result" } ], "source": [ "display(Markdown(\"### FSL BET\"))\n", "\n", "nv_FSL = AnyNiivue()\n", "nv_FSL.load_volumes([{\"path\": \"anat_bet.nii.gz\"}])\n", "nv_FSL" ] } ], "metadata": { "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": "3.11.6" } }, "nbformat": 4, "nbformat_minor": 4 }