![\"Open](\"https://colab.research.google.com/assets/colab-badge.svg\"){kind=icon}
+ 
+ 
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: 21%|██████▎ | 9.30M/44.3M [00:00<00:00, 92.9MB/s]
+Status: 54%|████████████████▊ | 24.0M/44.3M [00:00<00:00, 125MB/s]
+Status: 82%|█████████████████████████▌ | 36.5M/44.3M [00:00<00:00, 122MB/s]
+Status: 100%|███████████████████████████████| 44.3M/44.3M [00:00<00:00, 121MB/s]
+Creating temporary folder (/tmp/sct-20241017005027.449442-upud6xo2)
+Unzip data to: /tmp/sct-20241017005027.449442-upud6xo2
+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/tmpnhgyrqup/qc
+--
+Config deepseg_sc:
+ Centerline algorithm: svm
+ Brain in image: True
+ Kernel dimension: 2d
+ Contrast: t1
+ Threshold: 0.15
+Creating temporary folder (/tmp/sct-20241017005036.109654-rsbjre52)
+Reorient the image to RPI, if necessary...
+Finding the spinal cord centerline...
+Creating temporary folder (/tmp/sct-20241017005037.723751-07mknx7y)
+Remove temporary files...
+rm -rf /tmp/sct-20241017005037.723751-07mknx7y
+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<00:02, 5.47iter/s]
+Compute shape analysis: 100%|#################| 17/17 [00:00<00:00, 68.56iter/s]
+Remove temporary files...
+rm -rf /tmp/sct-20241017005036.109654-rsbjre52
+
+*** 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/tmpnhgyrqup/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/tmpnhgyrqup/qc/tmpnhgyrqup/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-20241017005050.435433-create_mask-izuszn2u)
+
+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-20241017005050.435433-create_mask-izuszn2u
+--
+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()
+
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+
+
+--
+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-20241017005100.639353-register-x5wdnejo)
+
+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-20241017005100.639353-register-x5wdnejo
+
+--
+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-20241017005100.639353-register-x5wdnejo
+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-20241017005101.291005-register-03lgs9vi)
+
+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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+/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-20241017005101.291005-register-03lgs9vi
+Merge warping fields along z...
+Move warping fields...
+cp step1Warp.nii.gz /tmp/sct-20241017005100.639353-register-x5wdnejo
+cp step1InverseWarp.nii.gz /tmp/sct-20241017005100.639353-register-x5wdnejo
+rm -rf /tmp/sct-20241017005101.291005-register-03lgs9vi
+
+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-20241017005100.639353-register-x5wdnejo
+/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-20241017005100.639353-register-x5wdnejo
+
+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-20241017005100.639353-register-x5wdnejo
+
+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-20241017005100.639353-register-x5wdnejo
+
+Generate output files...
+File created: mt0_reg.nii.gz
+mv /tmp/sct-20241017005100.639353-register-x5wdnejo/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-20241017005100.639353-register-x5wdnejo/warp_dest2src.nii.gz warp_t1w_crop2mt0.nii.gz
+File created: warp_t1w_crop2mt0.nii.gz
+
+Remove temporary files...
+rm -rf /tmp/sct-20241017005100.639353-register-x5wdnejo
+
+Finished! Elapsed time: 11s
+--
+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-20241017005118.646955-register-e_racygw)
+
+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-20241017005118.646955-register-e_racygw
+
+--
+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-20241017005118.646955-register-e_racygw
+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-20241017005119.199548-register-zuxf9378)
+
+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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+/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-20241017005119.199548-register-zuxf9378
+Merge warping fields along z...
+Move warping fields...
+cp step1Warp.nii.gz /tmp/sct-20241017005118.646955-register-e_racygw
+cp step1InverseWarp.nii.gz /tmp/sct-20241017005118.646955-register-e_racygw
+rm -rf /tmp/sct-20241017005119.199548-register-zuxf9378
+
+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-20241017005118.646955-register-e_racygw
+/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-20241017005118.646955-register-e_racygw
+
+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-20241017005118.646955-register-e_racygw
+
+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-20241017005118.646955-register-e_racygw
+
+Generate output files...
+File created: mt1_reg.nii.gz
+mv /tmp/sct-20241017005118.646955-register-e_racygw/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-20241017005118.646955-register-e_racygw/warp_dest2src.nii.gz warp_t1w_crop2mt1.nii.gz
+File created: warp_t1w_crop2mt1.nii.gz
+
+Remove temporary files...
+rm -rf /tmp/sct-20241017005118.646955-register-e_racygw
+
+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/tmpnhgyrqup/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/tmpnhgyrqup/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/tmpnhgyrqup/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/tmpnhgyrqup/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/tmpnhgyrqup/qc/tmpnhgyrqup/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
+ 9 # Loop across dic entries
+ 10 for i in range(len(plot_dic)+1):
+---> 11 df = pd.read_csv(plot_dic['file'][i])
+ 12 df.plot.bar(x='VertLevel', y='WA()', rot=0, ax=ax[i], legend=False)
+ 13 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)
+ 935 kwds_defaults = _refine_defaults_read(
+ 936 dialect,
+ 937 delimiter,
+ (...)
+ 944 dtype_backend=dtype_backend,
+ 945 )
+ 946 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)
+ 608 _validate_names(kwds.get("names", None))
+ 610 # Create the parser.
+--> 611 parser = TextFileReader(filepath_or_buffer, **kwds)
+ 613 if chunksize or iterator:
+ 614 return parser
+
+File ~/.local/lib/python3.10/site-packages/pandas/io/parsers/readers.py:1448, in TextFileReader.__init__(self, f, engine, **kwds)
+ 1445 self.options["has_index_names"] = kwds["has_index_names"]
+ 1447 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)
+ 1703 if "b" not in mode:
+ 1704 mode += "b"
+-> 1705 self.handles = get_handle(
+ 1706 f,
+ 1707 mode,
+ 1708 encoding=self.options.get("encoding", None),
+ 1709 compression=self.options.get("compression", None),
+ 1710 memory_map=self.options.get("memory_map", False),
+ 1711 is_text=is_text,
+ 1712 errors=self.options.get("encoding_errors", "strict"),
+ 1713 storage_options=self.options.get("storage_options", None),
+ 1714 )
+ 1715 assert self.handles is not None
+ 1716 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)
+ 858 elif isinstance(handle, str):
+ 859 # Check whether the filename is to be opened in binary mode.
+ 860 # Binary mode does not support 'encoding' and 'newline'.
+ 861 if ioargs.encoding and "b" not in ioargs.mode:
+ 862 # Encoding
+--> 863 handle = open(
+ 864 handle,
+ 865 ioargs.mode,
+ 866 encoding=ioargs.encoding,
+ 867 errors=errors,
+ 868 newline="",
+ 869 )
+ 870 else:
+ 871 # Binary mode
+ 872 handle = open(handle, ioargs.mode)
+
+FileNotFoundError: [Errno 2] No such file or directory: 'mtr_in_wm.csv'
+
+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]).
+