SCT Toolbox Example

SCT Toolbox Example#

Author: Steffen Bollmann

Setup Neurodesk#

%%capture
import os
import sys
IN_COLAB = 'google.colab' in sys.modules

if IN_COLAB:
  os.environ["LD_PRELOAD"] = "";
  os.environ["APPTAINER_BINDPATH"] = "/content,/tmp,/cvmfs"
  os.environ["MPLCONFIGDIR"] = "/content/matplotlib-mpldir"
  os.environ["LMOD_CMD"] = "/usr/share/lmod/lmod/libexec/lmod"

  !curl -J -O https://raw.githubusercontent.com/NeuroDesk/neurocommand/main/googlecolab_setup.sh
  !chmod +x googlecolab_setup.sh
  !./googlecolab_setup.sh

  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/')))))

# Output CPU information:
!cat /proc/cpuinfo | grep 'vendor' | uniq
!cat /proc/cpuinfo | grep 'model name' | uniq

vendor_id	: AuthenticAMD

model name	: AMD EPYC-Rome Processor

Demonstrating the Spinal Cord Toolbox (SCT) use via Neurodesk#

In Neurodesk we can use lmod to load specific versions of tools. Here we load the spinalcordtoolbox in a specific version:

import lmod
await lmod.load('spinalcordtoolbox/5.8')
await lmod.list()

['Lmod',
 'Warning:',
 'The',
 'environment',
 'MODULEPATH',
 'has',
 'been',
 'changed',
 'in',
 'unexpected',
 'ways.',
 'Lmod',
 'is',
 'unable',
 'to',
 'use',
 'given',
 'MODULEPATH.',
 'It',
 'is',
 'using:',
 '"/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/functional_imaging:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/rodent_imaging:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/image_registration:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/structural_imaging:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/image_segmentation:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/quantitative_imaging:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/workflows:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/hippocampus:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/image_reconstruction:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/data_organisation:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/electrophysiology:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/phase_processing:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/programming:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/machine_learning:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/diffusion_imaging:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/body:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/visualization:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/spectroscopy:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/quality_control:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/statistics:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/shape_analysis:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/spine:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/molecular_biology:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/bids_apps:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/cryo_EM:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/_diffusion_imaging:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/_functional_imaging:/cvmfs/neurodesk.ardc.edu.au/neurodesk-modules/_workflows::".',
 'Please',
 'use',
 '"module',
 'use',
 'to',
 'change',
 'MODULEPATH',
 'instead.',
 'spinalcordtoolbox/5.8']

In this interactive notebook we will go through a series of processing steps specific to spinal cord MRI analysis. We first need to import the necessary tools and setup the filenames and folders in the notebook environment.

The rest of this notebook is copied from the neurolibre project with minor path modifications and code adjustments to work with the current version of SCT: https://mathieuboudreau.github.io/pipelines-jupyter-book/01/sct_mtsat

%matplotlib inline
import matplotlib.pyplot as plt
import matplotlib.image as mpimg
import numpy as np
import sys
import os
from os.path import join
from IPython.display import clear_output

base_path = os.getcwd()

# Download example data
!sct_download_data -d sct_example_data -o ./sct_example_data

# Go to MT folder
os.chdir('./sct_example_data/mt/')

--
Spinal Cord Toolbox (5.8)

sct_download_data -d sct_example_data -o ./sct_example_data
--

Removing existing destination folder 'sct_example_data'
Trying URL: https://github.com/spinalcordtoolbox/sct_example_data/releases/download/r20180525/20180525_sct_example_data.zip

Downloading: 20180525_sct_example_data.zip

Status:   0%|                                       | 0.00/44.3M [00:00<?, ?B/s]

Status:   7%|██▏                           | 3.31M/44.3M [00:00<00:01, 32.7MB/s]

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Creating temporary folder (/tmp/sct-20241017002517.102143-f8lqg631)
Unzip data to: /tmp/sct-20241017002517.102143-f8lqg631

Copying data to: sct_example_data

Removing temporary folders...

Done!

# Jupyter Notebook config
verbose = True # False clears cells

# Folder/filename config
parent_dirs = os.path.split(base_path)
mt_folder_relative = os.path.join('sct_example_data/mt')
qc_path = os.path.join(base_path, 'qc')

t1w = 't1w'
mt0 = 'mt0'
mt1 = 'mt1'
label_c3c4 = 'label_c3c4'
warp_template2anat = 'warp_template2anat'
mtr = 'mtr'
mtsat = 'mtsat'
t1map = 't1map'

file_ext = '.nii.gz'

if not verbose:
    clear_output()

The first processing step consists in segmenting the spinal cord. This is done automatically using an algorithm called Optic that finds the spinal cord centerline, followed by a second algorithm called DeepSeg-SC that relies on deep learning for segmenting the cord.

# Segment spinal cord
!sct_deepseg_sc -i {t1w+file_ext} -c t1 -qc {qc_path}

if not verbose:
    clear_output()

--
Spinal Cord Toolbox (5.8)

sct_deepseg_sc -i t1w.nii.gz -c t1 -qc /storage/tmp/tmp7n28do3g/qc
--

Config deepseg_sc:
  Centerline algorithm: svm
  Brain in image: True
  Kernel dimension: 2d
  Contrast: t1
  Threshold: 0.15
Creating temporary folder (/tmp/sct-20241017002531.486770-04urbvxc)
Reorient the image to RPI, if necessary...

Finding the spinal cord centerline...

Creating temporary folder (/tmp/sct-20241017002532.938662-dxhd94nc)

Remove temporary files...
rm -rf /tmp/sct-20241017002532.938662-dxhd94nc

Cropping the image around the spinal cord...

Normalizing the intensity...

Segmenting the spinal cord using deep learning on 2D patches...

Reassembling the image...
Resampling the segmentation to the native image resolution using linear interpolation...

Binarizing the resampled segmentation...

Image header specifies datatype 'float32', but array is of type 'uint8'. Header metadata will be overwritten to use 'uint8'.

Compute shape analysis:   0%|                          | 0/17 [00:00<?, ?iter/s]

Compute shape analysis:   6%|#                 | 1/17 [00:00<00:07,  2.05iter/s]

Compute shape analysis: 100%|#################| 17/17 [00:00<00:00, 30.22iter/s]
Remove temporary files...
rm -rf /tmp/sct-20241017002531.486770-04urbvxc

*** Generate Quality Control (QC) html report ***
Resample images to 0.6x0.6 mm

Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Traceback (most recent call last):
  File "/opt/spinalcordtoolbox-5.8/spinalcordtoolbox/scripts/sct_deepseg_sc.py", line 214, in <module>
    main(sys.argv[1:])
  File "/opt/spinalcordtoolbox-5.8/spinalcordtoolbox/scripts/sct_deepseg_sc.py", line 207, in main
    generate_qc(fname_image, fname_seg=fname_seg, args=argv, path_qc=os.path.abspath(path_qc),
  File "/opt/spinalcordtoolbox-5.8/spinalcordtoolbox/reports/qc.py", line 851, in generate_qc
    add_entry(
  File "/opt/spinalcordtoolbox-5.8/spinalcordtoolbox/reports/qc.py", line 718, in add_entry
    layout(qcslice)
  File "/opt/spinalcordtoolbox-5.8/spinalcordtoolbox/reports/qc.py", line 290, in wrapped_f

    self.qc_report.make_content_path()
  File "/opt/spinalcordtoolbox-5.8/spinalcordtoolbox/reports/qc.py", line 604, in make_content_path
    raise err
  File "/opt/spinalcordtoolbox-5.8/spinalcordtoolbox/reports/qc.py", line 601, in make_content_path
    os.makedirs(target_img_folder, exist_ok=True)
  File "/opt/spinalcordtoolbox-5.8/python/envs/venv_sct/lib/python3.8/os.py", line 213, in makedirs
    makedirs(head, exist_ok=exist_ok)
  File "/opt/spinalcordtoolbox-5.8/python/envs/venv_sct/lib/python3.8/os.py", line 213, in makedirs
    makedirs(head, exist_ok=exist_ok)
  File "/opt/spinalcordtoolbox-5.8/python/envs/venv_sct/lib/python3.8/os.py", line 213, in makedirs
    makedirs(head, exist_ok=exist_ok)
  [Previous line repeated 2 more times]
  File "/opt/spinalcordtoolbox-5.8/python/envs/venv_sct/lib/python3.8/os.py", line 223, in makedirs
    mkdir(name, mode)
OSError: [Errno 30] Read-only file system: '/storage/tmp/tmp7n28do3g/qc'

Results of the segmentation appear in Figure 1.

# Plot QC figures

if sys.platform == 'darwin':
    # For local testing on OSX    
    sct_deepseg_sc_qc = 'qc/sct_example_data/mt/sct_deepseg_sc'
else:
    # For linux and on-line Binder execution
    sct_deepseg_sc_qc = join(qc_path, parent_dirs[-1], mt_folder_relative, 'sct_deepseg_sc')

folders = list(filter(lambda x: os.path.isdir(os.path.join(sct_deepseg_sc_qc, x)), os.listdir(sct_deepseg_sc_qc)))

qc_date = max(folders)

sct_deepseg_sc_qc_dir = join(sct_deepseg_sc_qc, qc_date)

bkg = mpimg.imread(join(sct_deepseg_sc_qc_dir, 'bkg_img.png'))
overlay = mpimg.imread(join(sct_deepseg_sc_qc_dir, 'overlay_img.png'))
plt.figure(figsize = (20,2))
plt.axis('off')
imgplot = plt.imshow(bkg)
imgplot = plt.imshow(overlay,alpha=0.3)

---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
Cell In[8], line 10
      6 else:
      7     # For linux and on-line Binder execution
      8     sct_deepseg_sc_qc = join(qc_path, parent_dirs[-1], mt_folder_relative, 'sct_deepseg_sc')
---> 10 folders = list(filter(lambda x: os.path.isdir(os.path.join(sct_deepseg_sc_qc, x)), os.listdir(sct_deepseg_sc_qc)))
     12 qc_date = max(folders)
     14 sct_deepseg_sc_qc_dir = join(sct_deepseg_sc_qc, qc_date)

FileNotFoundError: [Errno 2] No such file or directory: '/storage/tmp/tmp7n28do3g/qc/tmp7n28do3g/sct_example_data/mt/sct_deepseg_sc'

Figure 1. Quality control (QC) SCT module segmentation results. The segmentation (in red) is overlaid on the T1-weighted anatomical scan (in grayscale). Orientation is axial.

Using the generated segmentation, we create a mask around the spinal cord which will be used to crop the image for faster processing and more accurate registration results: the registration algorithm will concentrate on the spinal cord and not on the surrounding tissue (e.g., muscles, neck fat, etc.) which could move independently from the spinal cord and hence produce spurious motion correction results.

# Create mask
!sct_create_mask -i {t1w+file_ext} -p centerline,{t1w+'_seg'+file_ext} -size 35mm -o {t1w+'_mask'+file_ext}

# Crop data for faster processing
!sct_crop_image -i {t1w+file_ext} -m {t1w+'_mask'+file_ext} -o {t1w+'_crop'+file_ext}

if not verbose:
    clear_output()

--
Spinal Cord Toolbox (5.8)

sct_create_mask -i t1w.nii.gz -p centerline,t1w_seg.nii.gz -size 35mm -o t1w_mask.nii.gz
--

  OK: t1w_seg.nii.gz
Creating temporary folder (/tmp/sct-20241017002549.102831-create_mask-3dsg9lzp)

Orientation:
  LPI

Dimensions:
(192, 192, 22, 1, 0.8958333, 0.8958333, 5.000001, 1)

Create mask...
/opt/spinalcordtoolbox-5.8/spinalcordtoolbox/scripts/sct_create_mask.py:230: DeprecationWarning: get_header method is deprecated.
Please use the ``img.header`` property instead.

* deprecated from version: 2.1
* Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 4.0
  hdr = centerline.get_header()  # get header
/opt/spinalcordtoolbox-5.8/spinalcordtoolbox/scripts/sct_create_mask.py:233: DeprecationWarning: get_data() is deprecated in favor of get_fdata(), which has a more predictable return type. To obtain get_data() behavior going forward, use numpy.asanyarray(img.dataobj).

* deprecated from version: 3.0
* Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 5.0
  data_centerline = centerline.get_data()  # get centerline
/opt/spinalcordtoolbox-5.8/spinalcordtoolbox/scripts/sct_create_mask.py:245: DeprecationWarning: Please use `center_of_mass` from the `scipy.ndimage` namespace, the `scipy.ndimage.measurements` namespace is deprecated.
  cx[iz], cy[iz] = ndimage.measurements.center_of_mass(np.array(data_centerline[:, :, iz]))
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.

Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.
Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.

Image header specifies datatype 'int16', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'.

Remove temporary files...
rm -rf /tmp/sct-20241017002549.102831-create_mask-3dsg9lzp

--
Spinal Cord Toolbox (5.8)

sct_crop_image -i t1w.nii.gz -m t1w_mask.nii.gz -o t1w_crop.nii.gz
--

Bounding box: x=[73, 118], y=[69, 112], z=[4, 21]
Cropping the image...

Then, we register the proton density weighted (PD) image to the T1w image, and the MT-weighted image to the T1w image, so we end up with the T1w, MTw and PDw images all aligned together, which is a necessary condition for then computing quantitative MR metrics (here: MTsat).

# Register PD->T1w
# Tips: here we only use rigid transformation because both images have very similar sequence parameters. We don't want to use SyN/BSplineSyN to avoid introducing spurious deformations.
!sct_register_multimodal -i {mt0+file_ext} -d {t1w+'_crop'+file_ext} -param step=1,type=im,algo=rigid,slicewise=1,metric=CC -x spline

# Register MT->T1w
!sct_register_multimodal -i {mt1+file_ext} -d {t1w+'_crop'+file_ext} -param step=1,type=im,algo=rigid,slicewise=1,metric=CC -x spline

if not verbose:
    clear_output()

--
Spinal Cord Toolbox (5.8)

sct_register_multimodal -i mt0.nii.gz -d t1w_crop.nii.gz -param step=1,type=im,algo=rigid,slicewise=1,metric=CC -x spline
--

Input parameters:
  Source .............. mt0.nii.gz (192, 192, 22)
  Destination ......... t1w_crop.nii.gz (45, 43, 17)
  Init transfo ........ 
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...

Creating temporary folder (/tmp/sct-20241017002604.943771-register-7ua97w59)

Copying input data to tmp folder and convert to nii...

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MI[dest_RPI.nii,src.nii,1,32]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step0,src_regStep0.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20241017002604.943771-register-7ua97w59

--
ESTIMATE TRANSFORMATION FOR STEP #1

Apply transformation from previous step
/opt/spinalcordtoolbox-5.8/bin/isct_antsApplyTransforms -d 3 -i src.nii -o src_reg.nii -t warp_forward_0.nii.gz -r dest_RPI.nii -n 'BSpline[3]' # in /tmp/sct-20241017002604.943771-register-7ua97w59

Registration parameters:
  type ........... im
  algo ........... rigid
  slicewise ...... 1
  metric ......... CC
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 10
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca
Creating temporary folder (/tmp/sct-20241017002606.622418-register-ndz8_qa6)

Copy input data to temp folder...

Get image dimensions of destination image...
  matrix size: 45 x 43 x 17
  voxel size: 0.8958333mm x 0.8958333mm x 17mm

Split input volume...

Split destination volume...

Registering slice 0/16...
/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0000.nii,src_Z0000.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0000,src_Z0000_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0000.nii,src_Z0000.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00000Warp.nii.gz -R dest_Z0000.nii warp2d_null0Warp.nii.gz warp2d_00000GenericAffine.mat # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00000InverseWarp.nii.gz -R src_Z0000.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00000GenericAffine.mat # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

Registering slice 1/16...
/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0001.nii,src_Z0001.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0001,src_Z0001_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0001.nii,src_Z0001.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00010Warp.nii.gz -R dest_Z0001.nii warp2d_null0Warp.nii.gz warp2d_00010GenericAffine.mat # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00010InverseWarp.nii.gz -R src_Z0001.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00010GenericAffine.mat # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

Registering slice 2/16...
/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0002.nii,src_Z0002.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0002,src_Z0002_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0002.nii,src_Z0002.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00020Warp.nii.gz -R dest_Z0002.nii warp2d_null0Warp.nii.gz warp2d_00020GenericAffine.mat # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00020InverseWarp.nii.gz -R src_Z0002.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00020GenericAffine.mat # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

Registering slice 3/16...
/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0003.nii,src_Z0003.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0003,src_Z0003_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0003.nii,src_Z0003.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00030Warp.nii.gz -R dest_Z0003.nii warp2d_null0Warp.nii.gz warp2d_00030GenericAffine.mat # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00030InverseWarp.nii.gz -R src_Z0003.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00030GenericAffine.mat # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

Registering slice 4/16...
/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0004.nii,src_Z0004.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0004,src_Z0004_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0004.nii,src_Z0004.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00040Warp.nii.gz -R dest_Z0004.nii warp2d_null0Warp.nii.gz warp2d_00040GenericAffine.mat # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00040InverseWarp.nii.gz -R src_Z0004.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00040GenericAffine.mat # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

Registering slice 5/16...
/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0005.nii,src_Z0005.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0005,src_Z0005_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0005.nii,src_Z0005.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00050Warp.nii.gz -R dest_Z0005.nii warp2d_null0Warp.nii.gz warp2d_00050GenericAffine.mat # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00050InverseWarp.nii.gz -R src_Z0005.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00050GenericAffine.mat # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

Registering slice 6/16...
/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0006.nii,src_Z0006.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0006,src_Z0006_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0006.nii,src_Z0006.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00060Warp.nii.gz -R dest_Z0006.nii warp2d_null0Warp.nii.gz warp2d_00060GenericAffine.mat # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00060InverseWarp.nii.gz -R src_Z0006.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00060GenericAffine.mat # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

Registering slice 7/16...
/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0007.nii,src_Z0007.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0007,src_Z0007_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0007.nii,src_Z0007.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00070Warp.nii.gz -R dest_Z0007.nii warp2d_null0Warp.nii.gz warp2d_00070GenericAffine.mat # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00070InverseWarp.nii.gz -R src_Z0007.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00070GenericAffine.mat # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

Registering slice 8/16...
/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0008.nii,src_Z0008.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0008,src_Z0008_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0008.nii,src_Z0008.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00080Warp.nii.gz -R dest_Z0008.nii warp2d_null0Warp.nii.gz warp2d_00080GenericAffine.mat # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00080InverseWarp.nii.gz -R src_Z0008.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00080GenericAffine.mat # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

Registering slice 9/16...
/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0009.nii,src_Z0009.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0009,src_Z0009_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0009.nii,src_Z0009.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00090Warp.nii.gz -R dest_Z0009.nii warp2d_null0Warp.nii.gz warp2d_00090GenericAffine.mat # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00090InverseWarp.nii.gz -R src_Z0009.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00090GenericAffine.mat # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

Registering slice 10/16...
/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0010.nii,src_Z0010.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0010,src_Z0010_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0010.nii,src_Z0010.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00100Warp.nii.gz -R dest_Z0010.nii warp2d_null0Warp.nii.gz warp2d_00100GenericAffine.mat # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00100InverseWarp.nii.gz -R src_Z0010.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00100GenericAffine.mat # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

Registering slice 11/16...
/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0011.nii,src_Z0011.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0011,src_Z0011_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0011.nii,src_Z0011.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00110Warp.nii.gz -R dest_Z0011.nii warp2d_null0Warp.nii.gz warp2d_00110GenericAffine.mat # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00110InverseWarp.nii.gz -R src_Z0011.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00110GenericAffine.mat # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

Registering slice 12/16...
/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0012.nii,src_Z0012.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0012,src_Z0012_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0012.nii,src_Z0012.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00120Warp.nii.gz -R dest_Z0012.nii warp2d_null0Warp.nii.gz warp2d_00120GenericAffine.mat # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00120InverseWarp.nii.gz -R src_Z0012.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00120GenericAffine.mat # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

Registering slice 13/16...
/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0013.nii,src_Z0013.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0013,src_Z0013_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0013.nii,src_Z0013.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00130Warp.nii.gz -R dest_Z0013.nii warp2d_null0Warp.nii.gz warp2d_00130GenericAffine.mat # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00130InverseWarp.nii.gz -R src_Z0013.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00130GenericAffine.mat # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

Registering slice 14/16...
/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0014.nii,src_Z0014.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0014,src_Z0014_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0014.nii,src_Z0014.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00140Warp.nii.gz -R dest_Z0014.nii warp2d_null0Warp.nii.gz warp2d_00140GenericAffine.mat # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00140InverseWarp.nii.gz -R src_Z0014.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00140GenericAffine.mat # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

Registering slice 15/16...
/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0015.nii,src_Z0015.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0015,src_Z0015_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0015.nii,src_Z0015.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00150Warp.nii.gz -R dest_Z0015.nii warp2d_null0Warp.nii.gz warp2d_00150GenericAffine.mat # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00150InverseWarp.nii.gz -R src_Z0015.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00150GenericAffine.mat # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

Registering slice 16/16...
/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0016.nii,src_Z0016.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0016,src_Z0016_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0016.nii,src_Z0016.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00160Warp.nii.gz -R dest_Z0016.nii warp2d_null0Warp.nii.gz warp2d_00160GenericAffine.mat # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00160InverseWarp.nii.gz -R src_Z0016.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00160GenericAffine.mat # in /tmp/sct-20241017002606.622418-register-ndz8_qa6

Merge warping fields along z...

Move warping fields...
cp step1Warp.nii.gz /tmp/sct-20241017002604.943771-register-7ua97w59
cp step1InverseWarp.nii.gz /tmp/sct-20241017002604.943771-register-7ua97w59
rm -rf /tmp/sct-20241017002606.622418-register-ndz8_qa6

Concatenate transformations...
/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_1.nii.gz warp_forward_0.nii.gz # in /tmp/sct-20241017002604.943771-register-7ua97w59

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii warp_inverse_0.nii.gz warp_inverse_1.nii.gz # in /tmp/sct-20241017002604.943771-register-7ua97w59

Apply transfo source --> dest...
/opt/spinalcordtoolbox-5.8/bin/isct_antsApplyTransforms -d 3 -i src.nii -o src_reg.nii -t warp_src2dest.nii.gz -r dest.nii -n 'BSpline[3]' # in /tmp/sct-20241017002604.943771-register-7ua97w59


Apply transfo dest --> source...

/opt/spinalcordtoolbox-5.8/bin/isct_antsApplyTransforms -d 3 -i dest.nii -o dest_reg.nii -t warp_dest2src.nii.gz -r src.nii -n 'BSpline[3]' # in /tmp/sct-20241017002604.943771-register-7ua97w59

Generate output files...
File created: mt0_reg.nii.gz
mv /tmp/sct-20241017002604.943771-register-7ua97w59/warp_src2dest.nii.gz warp_mt02t1w_crop.nii.gz
File created: warp_mt02t1w_crop.nii.gz

File created: t1w_crop_reg.nii.gz
mv /tmp/sct-20241017002604.943771-register-7ua97w59/warp_dest2src.nii.gz warp_t1w_crop2mt0.nii.gz
File created: warp_t1w_crop2mt0.nii.gz

Remove temporary files...
rm -rf /tmp/sct-20241017002604.943771-register-7ua97w59

Finished! Elapsed time: 13s

--
Spinal Cord Toolbox (5.8)

sct_register_multimodal -i mt1.nii.gz -d t1w_crop.nii.gz -param step=1,type=im,algo=rigid,slicewise=1,metric=CC -x spline
--


Input parameters:

  Source .............. mt1.nii.gz (192, 192, 22)
  Destination ......... t1w_crop.nii.gz (45, 43, 17)
  Init transfo ........ 
  Mask ................ 
  Output name ......... 
  Remove temp files ... 1
  Verbose ............. 1

Check if input data are 3D...
Creating temporary folder (/tmp/sct-20241017002626.104288-register-f_qsa2qo)

Copying input data to tmp folder and convert to nii...

--
ESTIMATE TRANSFORMATION FOR STEP #0
Registration parameters:
  type ........... im
  algo ........... syn
  slicewise ...... 0
  metric ......... MI
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 0
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca

Estimate transformation
/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration --dimensionality 3 --transform 'syn[0.5,3,0]' --metric 'MI[dest_RPI.nii,src.nii,1,32]' --convergence 0 --shrink-factors 1 --smoothing-sigmas 0mm --restrict-deformation 1x1x0 --output '[step0,src_regStep0.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20241017002626.104288-register-f_qsa2qo

--
ESTIMATE TRANSFORMATION FOR STEP #1

Apply transformation from previous step
/opt/spinalcordtoolbox-5.8/bin/isct_antsApplyTransforms -d 3 -i src.nii -o src_reg.nii -t warp_forward_0.nii.gz -r dest_RPI.nii -n 'BSpline[3]' # in /tmp/sct-20241017002626.104288-register-f_qsa2qo

Registration parameters:
  type ........... im
  algo ........... rigid
  slicewise ...... 1
  metric ......... CC
  samplStrategy .. None
  samplPercent ... 0.2
  iter ........... 10
  smooth ......... 0
  laplacian ...... 0
  shrink ......... 1
  gradStep ....... 0.5
  deformation .... 1x1x0
  init ........... 
  poly ........... 5
  filter_size .... 5
  dof ............ Tx_Ty_Tz_Rx_Ry_Rz
  smoothWarpXY ... 2
  rot_method ..... pca
Creating temporary folder (/tmp/sct-20241017002626.712419-register-1kn5m7j5)

Copy input data to temp folder...

Get image dimensions of destination image...
  matrix size: 45 x 43 x 17
  voxel size: 0.8958333mm x 0.8958333mm x 17mm

Split input volume...

Split destination volume...

Registering slice 0/16...
/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0000.nii,src_Z0000.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0000,src_Z0000_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0000.nii,src_Z0000.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00000Warp.nii.gz -R dest_Z0000.nii warp2d_null0Warp.nii.gz warp2d_00000GenericAffine.mat # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00000InverseWarp.nii.gz -R src_Z0000.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00000GenericAffine.mat # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

Registering slice 1/16...
/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0001.nii,src_Z0001.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0001,src_Z0001_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0001.nii,src_Z0001.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00010Warp.nii.gz -R dest_Z0001.nii warp2d_null0Warp.nii.gz warp2d_00010GenericAffine.mat # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00010InverseWarp.nii.gz -R src_Z0001.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00010GenericAffine.mat # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

Registering slice 2/16...
/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0002.nii,src_Z0002.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0002,src_Z0002_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0002.nii,src_Z0002.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00020Warp.nii.gz -R dest_Z0002.nii warp2d_null0Warp.nii.gz warp2d_00020GenericAffine.mat # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00020InverseWarp.nii.gz -R src_Z0002.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00020GenericAffine.mat # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

Registering slice 3/16...
/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0003.nii,src_Z0003.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0003,src_Z0003_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0003.nii,src_Z0003.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00030Warp.nii.gz -R dest_Z0003.nii warp2d_null0Warp.nii.gz warp2d_00030GenericAffine.mat # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00030InverseWarp.nii.gz -R src_Z0003.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00030GenericAffine.mat # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

Registering slice 4/16...
/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0004.nii,src_Z0004.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0004,src_Z0004_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0004.nii,src_Z0004.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00040Warp.nii.gz -R dest_Z0004.nii warp2d_null0Warp.nii.gz warp2d_00040GenericAffine.mat # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00040InverseWarp.nii.gz -R src_Z0004.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00040GenericAffine.mat # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

Registering slice 5/16...
/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0005.nii,src_Z0005.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0005,src_Z0005_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0005.nii,src_Z0005.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00050Warp.nii.gz -R dest_Z0005.nii warp2d_null0Warp.nii.gz warp2d_00050GenericAffine.mat # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00050InverseWarp.nii.gz -R src_Z0005.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00050GenericAffine.mat # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

Registering slice 6/16...
/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0006.nii,src_Z0006.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0006,src_Z0006_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0006.nii,src_Z0006.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00060Warp.nii.gz -R dest_Z0006.nii warp2d_null0Warp.nii.gz warp2d_00060GenericAffine.mat # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00060InverseWarp.nii.gz -R src_Z0006.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00060GenericAffine.mat # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

Registering slice 7/16...
/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0007.nii,src_Z0007.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0007,src_Z0007_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0007.nii,src_Z0007.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00070Warp.nii.gz -R dest_Z0007.nii warp2d_null0Warp.nii.gz warp2d_00070GenericAffine.mat # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00070InverseWarp.nii.gz -R src_Z0007.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00070GenericAffine.mat # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

Registering slice 8/16...
/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0008.nii,src_Z0008.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0008,src_Z0008_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0008.nii,src_Z0008.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00080Warp.nii.gz -R dest_Z0008.nii warp2d_null0Warp.nii.gz warp2d_00080GenericAffine.mat # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00080InverseWarp.nii.gz -R src_Z0008.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00080GenericAffine.mat # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

Registering slice 9/16...
/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0009.nii,src_Z0009.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0009,src_Z0009_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0009.nii,src_Z0009.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00090Warp.nii.gz -R dest_Z0009.nii warp2d_null0Warp.nii.gz warp2d_00090GenericAffine.mat # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00090InverseWarp.nii.gz -R src_Z0009.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00090GenericAffine.mat # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

Registering slice 10/16...
/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0010.nii,src_Z0010.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0010,src_Z0010_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0010.nii,src_Z0010.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00100Warp.nii.gz -R dest_Z0010.nii warp2d_null0Warp.nii.gz warp2d_00100GenericAffine.mat # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00100InverseWarp.nii.gz -R src_Z0010.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00100GenericAffine.mat # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

Registering slice 11/16...
/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0011.nii,src_Z0011.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0011,src_Z0011_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0011.nii,src_Z0011.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00110Warp.nii.gz -R dest_Z0011.nii warp2d_null0Warp.nii.gz warp2d_00110GenericAffine.mat # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00110InverseWarp.nii.gz -R src_Z0011.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00110GenericAffine.mat # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

Registering slice 12/16...
/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0012.nii,src_Z0012.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0012,src_Z0012_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0012.nii,src_Z0012.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00120Warp.nii.gz -R dest_Z0012.nii warp2d_null0Warp.nii.gz warp2d_00120GenericAffine.mat # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00120InverseWarp.nii.gz -R src_Z0012.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00120GenericAffine.mat # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

Registering slice 13/16...
/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0013.nii,src_Z0013.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0013,src_Z0013_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0013.nii,src_Z0013.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00130Warp.nii.gz -R dest_Z0013.nii warp2d_null0Warp.nii.gz warp2d_00130GenericAffine.mat # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00130InverseWarp.nii.gz -R src_Z0013.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00130GenericAffine.mat # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

Registering slice 14/16...
/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0014.nii,src_Z0014.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0014,src_Z0014_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0014.nii,src_Z0014.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00140Warp.nii.gz -R dest_Z0014.nii warp2d_null0Warp.nii.gz warp2d_00140GenericAffine.mat # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00140InverseWarp.nii.gz -R src_Z0014.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00140GenericAffine.mat # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

Registering slice 15/16...
/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0015.nii,src_Z0015.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0015,src_Z0015_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0015.nii,src_Z0015.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00150Warp.nii.gz -R dest_Z0015.nii warp2d_null0Warp.nii.gz warp2d_00150GenericAffine.mat # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00150InverseWarp.nii.gz -R src_Z0015.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00150GenericAffine.mat # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

Registering slice 16/16...
/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'Rigid[0.5]' --metric 'CC[dest_Z0016.nii,src_Z0016.nii,1,4]' --convergence 10 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0016,src_Z0016_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_antsRegistration -d 2 -t 'SyN[1,1,1]' -c 0 -m 'MI[dest_Z0016.nii,src_Z0016.nii,1,32]' -o warp2d_null -f 1 -s 0 # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00160Warp.nii.gz -R dest_Z0016.nii warp2d_null0Warp.nii.gz warp2d_00160GenericAffine.mat # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 2 warp2d_00160InverseWarp.nii.gz -R src_Z0016.nii warp2d_null0InverseWarp.nii.gz -i warp2d_00160GenericAffine.mat # in /tmp/sct-20241017002626.712419-register-1kn5m7j5

Merge warping fields along z...

Move warping fields...
cp step1Warp.nii.gz /tmp/sct-20241017002626.104288-register-f_qsa2qo
cp step1InverseWarp.nii.gz /tmp/sct-20241017002626.104288-register-f_qsa2qo
rm -rf /tmp/sct-20241017002626.712419-register-1kn5m7j5

Concatenate transformations...
/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_1.nii.gz warp_forward_0.nii.gz # in /tmp/sct-20241017002626.104288-register-f_qsa2qo

/opt/spinalcordtoolbox-5.8/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii warp_inverse_0.nii.gz warp_inverse_1.nii.gz # in /tmp/sct-20241017002626.104288-register-f_qsa2qo

Apply transfo source --> dest...
/opt/spinalcordtoolbox-5.8/bin/isct_antsApplyTransforms -d 3 -i src.nii -o src_reg.nii -t warp_src2dest.nii.gz -r dest.nii -n 'BSpline[3]' # in /tmp/sct-20241017002626.104288-register-f_qsa2qo


Apply transfo dest --> source...

/opt/spinalcordtoolbox-5.8/bin/isct_antsApplyTransforms -d 3 -i dest.nii -o dest_reg.nii -t warp_dest2src.nii.gz -r src.nii -n 'BSpline[3]' # in /tmp/sct-20241017002626.104288-register-f_qsa2qo

Generate output files...
File created: mt1_reg.nii.gz
mv /tmp/sct-20241017002626.104288-register-f_qsa2qo/warp_src2dest.nii.gz warp_mt12t1w_crop.nii.gz
File created: warp_mt12t1w_crop.nii.gz
File t1w_crop_reg.nii.gz already exists. Deleting it..

File created: t1w_crop_reg.nii.gz
mv /tmp/sct-20241017002626.104288-register-f_qsa2qo/warp_dest2src.nii.gz warp_t1w_crop2mt1.nii.gz
File created: warp_t1w_crop2mt1.nii.gz

Remove temporary files...
rm -rf /tmp/sct-20241017002626.104288-register-f_qsa2qo

Finished! Elapsed time: 11s

Next step consists in registering the PAM50 template to the T1w image. We first create a label, centered in the spinal cord at level C3-C4 intervertebral disc, then we apply a multi-step non-linear registration algorithm.

# Create label 4 at the mid-FOV, because we know the FOV is centered at C3-C4 disc.
!sct_label_utils -i {t1w+'_seg'+file_ext} -create-seg-mid 4 -o {label_c3c4+file_ext}

# Register template->T1w_ax (using template-T1w as initial transformation)
!sct_register_to_template -i {t1w+'_crop'+file_ext} -s {t1w+'_seg'+file_ext} -ldisc {label_c3c4+file_ext} -ref subject -c t1 -param step=1,type=seg,algo=slicereg,metric=MeanSquares,smooth=2:step=2,type=im,algo=bsplinesyn,metric=MeanSquares,iter=5,gradStep=0.5 -qc {qc_path}

if not verbose:
    clear_output()

--
Spinal Cord Toolbox (5.8)

sct_label_utils -i t1w_seg.nii.gz -create-seg-mid 4 -o label_c3c4.nii.gz
--

Generating output files...

--
Spinal Cord Toolbox (5.8)

sct_register_to_template -i t1w_crop.nii.gz -s t1w_seg.nii.gz -ldisc label_c3c4.nii.gz -ref subject -c t1 -param step=1,type=seg,algo=slicereg,metric=MeanSquares,smooth=2:step=2,type=im,algo=bsplinesyn,metric=MeanSquares,iter=5,gradStep=0.5 -qc /storage/tmp/tmp7n28do3g/qc
--

Traceback (most recent call last):
  File "/opt/spinalcordtoolbox-5.8/spinalcordtoolbox/scripts/sct_register_to_template.py", line 817, in <module>
    main(sys.argv[1:])
  File "/opt/spinalcordtoolbox-5.8/spinalcordtoolbox/scripts/sct_register_to_template.py", line 304, in main
    arguments = parser.parse_args(argv)
  File "/opt/spinalcordtoolbox-5.8/python/envs/venv_sct/lib/python3.8/argparse.py", line 1768, in parse_args
    args, argv = self.parse_known_args(args, namespace)
  File "/opt/spinalcordtoolbox-5.8/python/envs/venv_sct/lib/python3.8/argparse.py", line 1800, in parse_known_args
    namespace, args = self._parse_known_args(args, namespace)
  File "/opt/spinalcordtoolbox-5.8/python/envs/venv_sct/lib/python3.8/argparse.py", line 2006, in _parse_known_args
    start_index = consume_optional(start_index)
  File "/opt/spinalcordtoolbox-5.8/python/envs/venv_sct/lib/python3.8/argparse.py", line 1946, in consume_optional
    take_action(action, args, option_string)
  File "/opt/spinalcordtoolbox-5.8/python/envs/venv_sct/lib/python3.8/argparse.py", line 1874, in take_action
    action(self, namespace, argument_values, option_string)
  File "/opt/spinalcordtoolbox-5.8/spinalcordtoolbox/utils/shell.py", line 230, in __call__
    folders = self.create_folder(values)
  File "/opt/spinalcordtoolbox-5.8/spinalcordtoolbox/utils/shell.py", line 223, in create_folder
    os.makedirs(folder_name, exist_ok=True)
  File "/opt/spinalcordtoolbox-5.8/python/envs/venv_sct/lib/python3.8/os.py", line 223, in makedirs
    mkdir(name, mode)
OSError: [Errno 30] Read-only file system: '/storage/tmp/tmp7n28do3g/qc'

Once the PAM50 is registered with the T1w image, we can warp all objects pertaining to the PAM50 into the T1w native space. These objects notably include a white matter atlas, which will be subsequently used to extract qMR metrics within specific white matter tracts.

# Warp template
!sct_warp_template -d {t1w+'_crop'+file_ext} -w {warp_template2anat+file_ext} -qc {qc_path}

if not verbose:
    clear_output()

--
Spinal Cord Toolbox (5.8)

sct_warp_template -d t1w_crop.nii.gz -w warp_template2anat.nii.gz -qc /storage/tmp/tmp7n28do3g/qc
--

Traceback (most recent call last):
  File "/opt/spinalcordtoolbox-5.8/spinalcordtoolbox/scripts/sct_warp_template.py", line 292, in <module>
    main(sys.argv[1:])
  File "/opt/spinalcordtoolbox-5.8/spinalcordtoolbox/scripts/sct_warp_template.py", line 235, in main
    arguments = parser.parse_args(argv)
  File "/opt/spinalcordtoolbox-5.8/python/envs/venv_sct/lib/python3.8/argparse.py", line 1768, in parse_args
    args, argv = self.parse_known_args(args, namespace)
  File "/opt/spinalcordtoolbox-5.8/python/envs/venv_sct/lib/python3.8/argparse.py", line 1800, in parse_known_args
    namespace, args = self._parse_known_args(args, namespace)
  File "/opt/spinalcordtoolbox-5.8/python/envs/venv_sct/lib/python3.8/argparse.py", line 2006, in _parse_known_args
    start_index = consume_optional(start_index)
  File "/opt/spinalcordtoolbox-5.8/python/envs/venv_sct/lib/python3.8/argparse.py", line 1946, in consume_optional
    take_action(action, args, option_string)
  File "/opt/spinalcordtoolbox-5.8/python/envs/venv_sct/lib/python3.8/argparse.py", line 1874, in take_action
    action(self, namespace, argument_values, option_string)
  File "/opt/spinalcordtoolbox-5.8/spinalcordtoolbox/utils/shell.py", line 230, in __call__
    folders = self.create_folder(values)
  File "/opt/spinalcordtoolbox-5.8/spinalcordtoolbox/utils/shell.py", line 223, in create_folder
    os.makedirs(folder_name, exist_ok=True)
  File "/opt/spinalcordtoolbox-5.8/python/envs/venv_sct/lib/python3.8/os.py", line 223, in makedirs
    mkdir(name, mode)
OSError: [Errno 30] Read-only file system: '/storage/tmp/tmp7n28do3g/qc'

Results of the registration/warming appear in Figure 2.

# Plot QC figures
if sys.platform == 'darwin':
    # For local testing on OSX    
    sct_warp_template_qc = 'qc/sct_example_data/mt/sct_warp_template'
else:
    # For linux and on-line Binder execution
    sct_warp_template_qc = join(qc_path, parent_dirs[-1],  mt_folder_relative, 'sct_warp_template')

folders = list(filter(lambda x: os.path.isdir(os.path.join(sct_warp_template_qc, x)), os.listdir(sct_warp_template_qc)))
qc_date = max(folders)

sct_warp_template_qc_dir = join(sct_warp_template_qc, qc_date)

bkg = mpimg.imread(join(sct_warp_template_qc_dir, 'bkg_img.png'))
overlay = mpimg.imread(join(sct_warp_template_qc_dir, 'overlay_img.png'))
plt.figure(figsize = (20,2))
plt.axis('off')
imgplot = plt.imshow(bkg)
imgplot = plt.imshow(overlay,alpha=0.3)

---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
Cell In[13], line 9
      5 else:
      6     # For linux and on-line Binder execution
      7     sct_warp_template_qc = join(qc_path, parent_dirs[-1],  mt_folder_relative, 'sct_warp_template')
----> 9 folders = list(filter(lambda x: os.path.isdir(os.path.join(sct_warp_template_qc, x)), os.listdir(sct_warp_template_qc)))
     10 qc_date = max(folders)
     12 sct_warp_template_qc_dir = join(sct_warp_template_qc, qc_date)

FileNotFoundError: [Errno 2] No such file or directory: '/storage/tmp/tmp7n28do3g/qc/tmp7n28do3g/sct_example_data/mt/sct_warp_template'

Figure 2. Quality control (QC) SCT module registration/warping results of the PAM50 template and atlas to the T1w native space. The white matter (in blue) is overlaid on the T1-weighted anatomical scan (in grayscale). Orientation is axial.Once co-registration between images and registration to the template is complete, we can venture into computing our favorite qMR metrics. Here, we compute the magnetization transfer ratio (MTR) and the magnetization transfer saturation (MTsat).

Once co-registration between images and registration to the template is complete, we can venture into computing our favorite qMR metrics. Here, we compute the magnetization transfer ratio (MTR) and the magnetization transfer saturation (MTsat).

# Compute MTR
!sct_compute_mtr -mt1 {mt1+'_reg'+file_ext} -mt0 {mt0+'_reg'+file_ext}

# Compute MTsat and T1
!sct_compute_mtsat -mt {mt1+'_reg'+file_ext} -pd {mt0+'_reg'+file_ext} -t1 {t1w+'_crop'+file_ext} -trmt 57 -trpd 57 -trt1 15 -famt 9 -fapd 9 -fat1 15

if not verbose:
    clear_output()

--
Spinal Cord Toolbox (5.8)

sct_compute_mtr -mt1 mt1_reg.nii.gz -mt0 mt0_reg.nii.gz
--


Compute MTR...
Found 0 voxels with value=0. These will be replaced by nan.
Threshold to clip values: +/- 100

--
Spinal Cord Toolbox (5.8)

sct_compute_mtsat -mt mt1_reg.nii.gz -pd mt0_reg.nii.gz -t1 t1w_crop.nii.gz -trmt 57 -trpd 57 -trt1 15 -famt 9 -fapd 9 -fat1 15
--

Load data...
Compute T1 map...
R1 values were found to be lower than 0.01. They will be set to inf, producing T1=0 for these voxels.
Compute A...
Compute MTsat...
MTsat values were found to be larger than 1. They will be set to zero for these voxels.
Generate output files...

Now that our metrics are computed, we want to extract their values within specific tracts of the spinal cord. This is done with the function sct_extract_metric.

# Extract MTR, MTsat and T1 in WM between C2 and C4 vertebral levels
!sct_extract_metric -i mtr.nii.gz -l 51 -vert 2:4 -perlevel 1 -o mtr_in_wm.csv
!sct_extract_metric -i mtsat.nii.gz -l 51 -vert 2:4 -perlevel 1 -o mtsat_in_wm.csv
!sct_extract_metric -i t1map.nii.gz -l 51 -vert 2:4 -perlevel 1 -o t1_in_wm.csv

if not verbose:
    clear_output()

--
Spinal Cord Toolbox (5.8)

sct_extract_metric -i mtr.nii.gz -l 51 -vert 2:4 -perlevel 1 -o mtr_in_wm.csv
--

Traceback (most recent call last):
  File "/opt/spinalcordtoolbox-5.8/spinalcordtoolbox/scripts/sct_extract_metric.py", line 397, in <module>
    main(sys.argv[1:])
  File "/opt/spinalcordtoolbox-5.8/spinalcordtoolbox/scripts/sct_extract_metric.py", line 348, in main
    raise RuntimeError(path_label + ' does not exist')
RuntimeError: label/atlas does not exist

--
Spinal Cord Toolbox (5.8)

sct_extract_metric -i mtsat.nii.gz -l 51 -vert 2:4 -perlevel 1 -o mtsat_in_wm.csv
--

Traceback (most recent call last):
  File "/opt/spinalcordtoolbox-5.8/spinalcordtoolbox/scripts/sct_extract_metric.py", line 397, in <module>
    main(sys.argv[1:])
  File "/opt/spinalcordtoolbox-5.8/spinalcordtoolbox/scripts/sct_extract_metric.py", line 348, in main
    raise RuntimeError(path_label + ' does not exist')
RuntimeError: label/atlas does not exist

--
Spinal Cord Toolbox (5.8)

sct_extract_metric -i t1map.nii.gz -l 51 -vert 2:4 -perlevel 1 -o t1_in_wm.csv
--

Traceback (most recent call last):
  File "/opt/spinalcordtoolbox-5.8/spinalcordtoolbox/scripts/sct_extract_metric.py", line 397, in <module>
    main(sys.argv[1:])
  File "/opt/spinalcordtoolbox-5.8/spinalcordtoolbox/scripts/sct_extract_metric.py", line 348, in main
    raise RuntimeError(path_label + ' does not exist')
RuntimeError: label/atlas does not exist

Results are output as csv files, which we can then open and display as bar graphs.

!pip install pandas

Defaulting to user installation because normal site-packages is not writeable

Requirement already satisfied: pandas in /home/ubuntu/.local/lib/python3.10/site-packages (2.1.4)

Requirement already satisfied: numpy<2,>=1.22.4 in /home/ubuntu/.local/lib/python3.10/site-packages (from pandas) (1.26.2)
Requirement already satisfied: python-dateutil>=2.8.2 in /home/ubuntu/.local/lib/python3.10/site-packages (from pandas) (2.8.2)
Requirement already satisfied: pytz>=2020.1 in /usr/lib/python3/dist-packages (from pandas) (2022.1)
Requirement already satisfied: tzdata>=2022.1 in /home/ubuntu/.local/lib/python3.10/site-packages (from pandas) (2023.3)
Requirement already satisfied: six>=1.5 in /usr/lib/python3/dist-packages (from python-dateutil>=2.8.2->pandas) (1.16.0)

WARNING: Error parsing dependencies of distro-info: Invalid version: '1.1build1'
WARNING: Error parsing dependencies of python-debian: Invalid version: '0.1.43ubuntu1'

# Display plots of results
import pandas as pd
fig, ax = plt.subplots(ncols=3, figsize=(15,4))

# Build dic for plot
plot_dic = {'file': ['mtr_in_wm.csv', 'mtsat_in_wm.csv', 't1_in_wm.csv'],
            'ylabel': ['MTR [%]', 'MTsat [a.u.]', 'T1 [s]']}

# Loop across dic entries
for i in range(len(plot_dic)+1):
    df = pd.read_csv(plot_dic['file'][i])
    df.plot.bar(x='VertLevel', y='WA()', rot=0, ax=ax[i], legend=False)
    ax[i].set_ylabel(plot_dic['ylabel'][i])
    ax[i].yaxis.grid()

---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
Cell In[17], line 11
# Loop across dic entries
for i in range(len(plot_dic)+1):
---> 11     df = pd.read_csv(plot_dic['file'][i])
   df.plot.bar(x='VertLevel', y='WA()', rot=0, ax=ax[i], legend=False)
   ax[i].set_ylabel(plot_dic['ylabel'][i])

File ~/.local/lib/python3.10/site-packages/pandas/io/parsers/readers.py:948, in read_csv(filepath_or_buffer, sep, delimiter, header, names, index_col, usecols, dtype, engine, converters, true_values, false_values, skipinitialspace, skiprows, skipfooter, nrows, na_values, keep_default_na, na_filter, verbose, skip_blank_lines, parse_dates, infer_datetime_format, keep_date_col, date_parser, date_format, dayfirst, cache_dates, iterator, chunksize, compression, thousands, decimal, lineterminator, quotechar, quoting, doublequote, escapechar, comment, encoding, encoding_errors, dialect, on_bad_lines, delim_whitespace, low_memory, memory_map, float_precision, storage_options, dtype_backend)
kwds_defaults = _refine_defaults_read(
   dialect,
   delimiter,
   (...)
   dtype_backend=dtype_backend,
)
kwds.update(kwds_defaults)
--> 948 return _read(filepath_or_buffer, kwds)

File ~/.local/lib/python3.10/site-packages/pandas/io/parsers/readers.py:611, in _read(filepath_or_buffer, kwds)
_validate_names(kwds.get("names", None))
# Create the parser.
--> 611 parser = TextFileReader(filepath_or_buffer, **kwds)
if chunksize or iterator:
   return parser

File ~/.local/lib/python3.10/site-packages/pandas/io/parsers/readers.py:1448, in TextFileReader.__init__(self, f, engine, **kwds)
   self.options["has_index_names"] = kwds["has_index_names"]
self.handles: IOHandles | None = None
-> 1448 self._engine = self._make_engine(f, self.engine)

File ~/.local/lib/python3.10/site-packages/pandas/io/parsers/readers.py:1705, in TextFileReader._make_engine(self, f, engine)
   if "b" not in mode:
       mode += "b"
-> 1705 self.handles = get_handle(
   f,
   mode,
   encoding=self.options.get("encoding", None),
   compression=self.options.get("compression", None),
   memory_map=self.options.get("memory_map", False),
   is_text=is_text,
   errors=self.options.get("encoding_errors", "strict"),
   storage_options=self.options.get("storage_options", None),
)
assert self.handles is not None
f = self.handles.handle

File ~/.local/lib/python3.10/site-packages/pandas/io/common.py:863, in get_handle(path_or_buf, mode, encoding, compression, memory_map, is_text, errors, storage_options)
elif isinstance(handle, str):
   # Check whether the filename is to be opened in binary mode.
   # Binary mode does not support 'encoding' and 'newline'.
   if ioargs.encoding and "b" not in ioargs.mode:
       # Encoding
--> 863         handle = open(
           handle,
           ioargs.mode,
           encoding=ioargs.encoding,
           errors=errors,
           newline="",
       )
   else:
       # Binary mode
       handle = open(handle, ioargs.mode)

FileNotFoundError: [Errno 2] No such file or directory: 'mtr_in_wm.csv'

_images/bc215981e109743989603d8d1c8ae9359f60763287ca50d32a1b16995c782e08.png

Figure 3. Quantitative MRI metrics in WM between C2 and C4 vertebral levels. The three calculated metrics from this dataset using SCT are the magnetization transfer ratio (MTR – [%]), magnetization transfer saturation (MTsat – [a.u.]), and longitudinal relaxation time (T1 – [s]).

SCT Toolbox Example

Contents

SCT Toolbox Example#

Setup Neurodesk#

Demonstrating the Spinal Cord Toolbox (SCT) use via Neurodesk#