+ set -e -o pipefail + trap 'echo Caught Keyboard Interrupt within script. Exiting now.; exit' INT + echo 'Retrieved variables from from the caller sct_run_batch:' Retrieved variables from from the caller sct_run_batch: + echo 'PATH_DATA: /Users/fmuhamma/Desktop/Mri/BIDS/sourcedata' PATH_DATA: /Users/fmuhamma/Desktop/Mri/BIDS/sourcedata + echo 'PATH_DATA_PROCESSED: /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed' PATH_DATA_PROCESSED: /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed + echo 'PATH_RESULTS: /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/results' PATH_RESULTS: /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/results + echo 'PATH_LOG: /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/log' PATH_LOG: /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/log + echo 'PATH_QC: /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc' PATH_QC: /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc ++ dirname /Users/fmuhamma/Desktop/Mri/BIDS/sourcedata + path_source=/Users/fmuhamma/Desktop/Mri/BIDS + PATH_DERIVATIVES=/Users/fmuhamma/Desktop/Mri/BIDS/derivatives/labels + PATH_SCRIPTS=/Users/FMUHAMMA/Desktop/Mri + SUBJECT=sub-CSM070/ses-spinalcord + cd /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed + rsync -Ravzh /Users/fmuhamma/Desktop/Mri/BIDS/sourcedata/./sub-CSM070/ses-spinalcord . building file list ... done sub-CSM070/ses-spinalcord/ sub-CSM070/ses-spinalcord/.DS_Store sub-CSM070/ses-spinalcord/anat/ sub-CSM070/ses-spinalcord/anat/sub-CSM070_ses-spinalcord_3DMAGiC.nii.gz sub-CSM070/ses-spinalcord/anat/sub-CSM070_ses-spinalcord_T2star.nii.gz sub-CSM070/ses-spinalcord/anat/sub-CSM070_ses-spinalcord_T2w.nii.gz sub-CSM070/ses-spinalcord/anat/sub-CSM070_ses-spinalcord_acq-MToff_MTS.nii.gz sub-CSM070/ses-spinalcord/anat/sub-CSM070_ses-spinalcord_acq-MTon_MTS.nii.gz sub-CSM070/ses-spinalcord/anat/sub-CSM070_ses-spinalcord_acq-T1w_MTS.nii.gz sub-CSM070/ses-spinalcord/dwi/ sub-CSM070/ses-spinalcord/func/ sub-CSM070/ses-spinalcord/func/sub-CSM070_ses-spinalcord_task-stim_run0_ECG.1D sub-CSM070/ses-spinalcord/func/sub-CSM070_ses-spinalcord_task-stim_run0_Resp.1D sub-CSM070/ses-spinalcord/func/sub-CSM070_ses-spinalcord_task-stim_run0_bold.nii.gz sub-CSM070/ses-spinalcord/func/sub-CSM070_ses-spinalcord_task-stim_run1_ECG.1D sub-CSM070/ses-spinalcord/func/sub-CSM070_ses-spinalcord_task-stim_run1_Resp.1D sub-CSM070/ses-spinalcord/func/sub-CSM070_ses-spinalcord_task-stim_run1_bold.nii.gz sub-CSM070/ses-spinalcord/func/sub-CSM070_ses-spinalcord_task-stim_run2_ECG.1D sub-CSM070/ses-spinalcord/func/sub-CSM070_ses-spinalcord_task-stim_run2_Resp.1D sub-CSM070/ses-spinalcord/func/sub-CSM070_ses-spinalcord_task-stim_run2_bold.nii.gz sub-CSM070/ses-spinalcord/func/sub-CSM070_ses-spinalcord_task-stim_run3_ECG.1D sub-CSM070/ses-spinalcord/func/sub-CSM070_ses-spinalcord_task-stim_run3_Resp.1D sub-CSM070/ses-spinalcord/func/sub-CSM070_ses-spinalcord_task-stim_run3_bold.nii.gz sent 167.93M bytes received 462 bytes 37.32M bytes/sec total size is 169.47M speedup is 1.01 + cd sub-CSM070/ses-spinalcord/anat + file=sub-CSM070_ses-spinalcord ++ basename sub-CSM070/ses-spinalcord + SES=ses-spinalcord + [[ ses-spinalcord == *\s\p\i\n\a\l\c\o\r\d* ]] + file_t2w=sub-CSM070_ses-spinalcord_T2w + [[ -f sub-CSM070_ses-spinalcord_T2w.nii.gz ]] + mkdir -p /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w + cp sub-CSM070_ses-spinalcord_T2w.nii.gz /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w + cd T2w + segment_if_does_not_exist sub-CSM070_ses-spinalcord_T2w t2 deepseg anat + local file=sub-CSM070_ses-spinalcord_T2w + local contrast=t2 + local segmentation_method=deepseg + local subfolder=anat + FILESEG=sub-CSM070_ses-spinalcord_T2w_seg + FILESEGMANUAL=/Users/fmuhamma/Desktop/Mri/BIDS/derivatives/labels/sub-CSM070/ses-spinalcord/ses-spinalcord/anat/sub-CSM070_ses-spinalcord_T2w_seg.nii.gz + echo + echo 'Looking for manual segmentation: /Users/fmuhamma/Desktop/Mri/BIDS/derivatives/labels/sub-CSM070/ses-spinalcord/ses-spinalcord/anat/sub-CSM070_ses-spinalcord_T2w_seg.nii.gz' Looking for manual segmentation: /Users/fmuhamma/Desktop/Mri/BIDS/derivatives/labels/sub-CSM070/ses-spinalcord/ses-spinalcord/anat/sub-CSM070_ses-spinalcord_T2w_seg.nii.gz + [[ -e /Users/fmuhamma/Desktop/Mri/BIDS/derivatives/labels/sub-CSM070/ses-spinalcord/ses-spinalcord/anat/sub-CSM070_ses-spinalcord_T2w_seg.nii.gz ]] + echo 'Not found. Proceeding with automatic segmentation.' Not found. Proceeding with automatic segmentation. + [[ deepseg == \d\e\e\p\s\e\g ]] + sct_deepseg_sc -i sub-CSM070_ses-spinalcord_T2w.nii.gz -c t2 -qc /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc -qc-subject sub-CSM070/ses-spinalcord -- Spinal Cord Toolbox (6.0) sct_deepseg_sc -i sub-CSM070_ses-spinalcord_T2w.nii.gz -c t2 -qc /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc -qc-subject sub-CSM070/ses-spinalcord -- Config deepseg_sc: Centerline algorithm: svm Brain in image: True Kernel dimension: 2d Contrast: t2 Threshold: 0.7 Creating temporary folder (/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-41-37_deepseg-sc_v7vfd6nx) Reorient the image to RPI, if necessary... Finding the spinal cord centerline... Creating temporary folder (/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-41-38_optic-detect-centerline__5i1_4k7) Remove temporary files... rm -rf /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-41-38_optic-detect-centerline__5i1_4k7 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... Removing small objects above slice #254 Removing small objects above slice #254 Removing small objects above slice #254 Image header specifies datatype 'float32', but array is of type 'uint8'. Header metadata will be overwritten to use 'uint8'. Remove temporary files... rm -rf /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-41-37_deepseg-sc_v7vfd6nx *** 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'. QcImage: layout with Axial slice Compute center of mass at each slice /Users/FMUHAMMA/sct_6.0/python/envs/venv_sct/lib/python3.9/site-packages/scipy/ndimage/_measurements.py:1535: RuntimeWarning: invalid value encountered in double_scalars results = [sum(input * grids[dir].astype(float), labels, index) / normalizer /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/ses-spinalcord/sub-CSM070/ses-spinalcord/T2w/sct_deepseg_sc/2023_11_14_154152.993793/background_img.png cp /Users/fmuhamma/sct_6.0/spinalcordtoolbox/reports/assets/_assets/css/bootstrap.min.css /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/_assets/css cp /Users/fmuhamma/sct_6.0/spinalcordtoolbox/reports/assets/_assets/css/bootstrap-table.min.css /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/_assets/css cp /Users/fmuhamma/sct_6.0/spinalcordtoolbox/reports/assets/_assets/css/bootstrap.min.css.map /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/_assets/css cp /Users/fmuhamma/sct_6.0/spinalcordtoolbox/reports/assets/_assets/css/style.css /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/_assets/css cp /Users/fmuhamma/sct_6.0/spinalcordtoolbox/reports/assets/_assets/js/filesaver.min.js /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/_assets/js cp /Users/fmuhamma/sct_6.0/spinalcordtoolbox/reports/assets/_assets/js/jquery-3.1.0.min.js /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/_assets/js cp /Users/fmuhamma/sct_6.0/spinalcordtoolbox/reports/assets/_assets/js/bootstrap-table.min.js /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/_assets/js cp /Users/fmuhamma/sct_6.0/spinalcordtoolbox/reports/assets/_assets/js/main.js /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/_assets/js cp /Users/fmuhamma/sct_6.0/spinalcordtoolbox/reports/assets/_assets/js/bootstrap.min.js /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/_assets/js cp /Users/fmuhamma/sct_6.0/spinalcordtoolbox/reports/assets/_assets/js/yaml.min.js /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/_assets/js cp /Users/fmuhamma/sct_6.0/spinalcordtoolbox/reports/assets/_assets/imgs/f-icon.png /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/_assets/imgs cp /Users/fmuhamma/sct_6.0/spinalcordtoolbox/reports/assets/_assets/imgs/keyright.png /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/_assets/imgs cp /Users/fmuhamma/sct_6.0/spinalcordtoolbox/reports/assets/_assets/imgs/keydown.png /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/_assets/imgs cp /Users/fmuhamma/sct_6.0/spinalcordtoolbox/reports/assets/_assets/imgs/keyup.png /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/_assets/imgs cp /Users/fmuhamma/sct_6.0/spinalcordtoolbox/reports/assets/_assets/imgs/sct_logo.png /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/_assets/imgs cp /Users/fmuhamma/sct_6.0/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.woff /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/_assets/fonts cp /Users/fmuhamma/sct_6.0/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.eot /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/_assets/fonts cp /Users/fmuhamma/sct_6.0/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.woff2 /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/_assets/fonts cp /Users/fmuhamma/sct_6.0/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.ttf /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/_assets/fonts cp /Users/fmuhamma/sct_6.0/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.svg /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/_assets/fonts Successfully generated the QC results in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/_json/qc_2023_11_14_154152.993793.json To see the results in a browser, type: open /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/index.html Done! To view results, run one of the following commands (depending on your preferred viewer): fsleyes sub-CSM070_ses-spinalcord_T2w.nii.gz -cm greyscale sub-CSM070_ses-spinalcord_T2w_seg.nii.gz -cm red -a 70.0 & fslview_deprecated sub-CSM070_ses-spinalcord_T2w.nii.gz -l Greyscale sub-CSM070_ses-spinalcord_T2w_seg.nii.gz -l Red -t 0.7 & fslview sub-CSM070_ses-spinalcord_T2w.nii.gz -l Greyscale sub-CSM070_ses-spinalcord_T2w_seg.nii.gz -l Red -t 0.7 & + file_t2_seg=sub-CSM070_ses-spinalcord_T2w_seg + label_if_does_not_exist sub-CSM070_ses-spinalcord_T2w sub-CSM070_ses-spinalcord_T2w_seg + local file=sub-CSM070_ses-spinalcord_T2w + local file_seg=sub-CSM070_ses-spinalcord_T2w_seg + FILELABEL=sub-CSM070_ses-spinalcord_T2w_labels-disc + FILELABELMANUAL=/Users/fmuhamma/Desktop/Mri/BIDS/derivatives/labels/sub-CSM070/ses-spinalcord/anat/sub-CSM070_ses-spinalcord_T2w_labels-disc-manual.nii.gz + echo 'Looking for manual label: /Users/fmuhamma/Desktop/Mri/BIDS/derivatives/labels/sub-CSM070/ses-spinalcord/anat/sub-CSM070_ses-spinalcord_T2w_labels-disc-manual.nii.gz' Looking for manual label: /Users/fmuhamma/Desktop/Mri/BIDS/derivatives/labels/sub-CSM070/ses-spinalcord/anat/sub-CSM070_ses-spinalcord_T2w_labels-disc-manual.nii.gz + [[ -e /Users/fmuhamma/Desktop/Mri/BIDS/derivatives/labels/sub-CSM070/ses-spinalcord/anat/sub-CSM070_ses-spinalcord_T2w_labels-disc-manual.nii.gz ]] + echo 'Not found. Proceeding with automatic labeling.' Not found. Proceeding with automatic labeling. + sct_label_vertebrae -i sub-CSM070_ses-spinalcord_T2w.nii.gz -s sub-CSM070_ses-spinalcord_T2w_seg.nii.gz -c t2 -qc /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc -qc-subject sub-CSM070/ses-spinalcord -- Spinal Cord Toolbox (6.0) sct_label_vertebrae -i sub-CSM070_ses-spinalcord_T2w.nii.gz -s sub-CSM070_ses-spinalcord_T2w_seg.nii.gz -c t2 -qc /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc -qc-subject sub-CSM070/ses-spinalcord -- Creating temporary folder (/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-41-55_label-vertebrae_glj_9nxn) Copying input data to tmp folder... Straighten spinal cord... Creating temporary folder (/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-41-55_straighten-spinalcord_rpfwfdu8) Copy files to tmp folder... Fitting centerline using B-spline approximation Error on approximation = 3.3 mm Error on approximation = 1.09 mm Error on approximation = 0.93 mm Error on approximation = 0.55 mm Error on approximation = 0.43 mm Error on approximation = 0.4 mm Error on approximation = 0.38 mm Error on approximation = 0.37 mm Error on approximation = 0.38 mm Error on approximation = 0.37 mm Error on approximation = 0.36 mm Error on approximation = 0.33 mm Error on approximation = 0.31 mm Error on approximation = 0.28 mm Error on approximation = 0.26 mm Error on approximation = 0.25 mm Error on approximation = 0.26 mm Error on approximation = 0.26 mm Error on approximation = 0.26 mm Error on approximation = 0.25 mm Error on approximation = 0.23 mm Error on approximation = 0.22 mm Error on approximation = 0.2 mm Error on approximation = 0.19 mm Error on approximation = 0.18 mm Error on approximation = 0.17 mm Error on approximation = 0.16 mm Error on approximation = 0.15 mm Error on approximation = 0.15 mm Error on approximation = 0.14 mm Error on approximation = 0.13 mm Error on approximation = 0.13 mm Create the straight space and the safe zone Length of spinal cord: 224.69547121164302 Size of spinal cord in z direction: 203.33220199631953 Ratio length/size: 1.1050658430173799 Safe zone boundaries (curved space): [-120.62283126400612, 82.7093707323134] Safe zone boundaries (straight space): [-131.30446587166784, 93.39100533997514] Pad input volume to account for spinal cord length... Time to generate centerline: 16.0 ms Warping field generated: tmp.curve2straight.nii.gz Warping field generated: tmp.straight2curve.nii.gz Apply transformation to input image... /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i data.nii -o tmp.anat_rigid_warp.nii.gz -t tmp.curve2straight.nii.gz -r tmp.centerline_pad_crop.nii.gz -n 'BSpline[3]' # in /private/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-41-55_straighten-spinalcord_rpfwfdu8 Generate output files... mv /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-41-55_straighten-spinalcord_rpfwfdu8/tmp.curve2straight.nii.gz ./warp_curve2straight.nii.gz File created: ./warp_curve2straight.nii.gz mv /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-41-55_straighten-spinalcord_rpfwfdu8/tmp.straight2curve.nii.gz ./warp_straight2curve.nii.gz File created: ./warp_straight2curve.nii.gz cp /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-41-55_straighten-spinalcord_rpfwfdu8/tmp.anat_rigid_warp.nii.gz ./straight_ref.nii.gz File created: ./data_straight.nii Remove temporary files... rm -rf /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-41-55_straighten-spinalcord_rpfwfdu8 Resample to 0.5mm isotropic... load data... Apply straightening to segmentation... /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i segmentation.nii -o segmentation_straight.nii -t warp_curve2straight.nii.gz -r data_straightr.nii -n Linear # in /private/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-41-55_label-vertebrae_glj_9nxn File /private/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-41-55_label-vertebrae_glj_9nxn/segmentation_straight.nii already exists. Will overwrite it. Create label to identify disc... Creating temporary folder... Creating temporary folder (/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-42-34_detect-c2c3_qy8wee0o) Run C2-C3 detector... C2-C3 detected... Remove temporary files... rm -rf /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-42-34_detect-c2c3_qy8wee0o File /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-41-55_label-vertebrae_glj_9nxn/labelz.nii.gz already exists. Will overwrite it. And apply straightening to label... /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i labelz.nii.gz -o labelz_straight.nii.gz -t warp_curve2straight.nii.gz -r data_straightr.nii -n NearestNeighbor # in /private/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-41-55_label-vertebrae_glj_9nxn Get z and disc values from straight label... .. [355, 3] Look for template... Path template: /Users/fmuhamma/sct_6.0/data/PAM50 Open template and vertebral levels... Disc values from template: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] Z-values for each disc: [963, 938, 907, 870, 833, 800, 769, 735, 692, 646, 600, 551, 500, 449, 396, 342, 289, 231, 168, 104, 79] Distances between discs (in voxel): [25.0, 31.0, 37.0, 37.0, 33.0, 31.0, 34.0, 43.0, 46.0, 46.0, 49.0, 51.0, 51.0, 53.0, 54.0, 53.0, 58.0, 63.0, 64.0, 25.0] Detect intervertebral discs... Current disc: 2 (z=355). Direction: superior .. Peak found: z=-5 (correlation = 0.390651516041429) Current disc: 1 (z=381). Direction: superior .. correcting factor: 1.0 .. Switching to inferior direction. Current disc: 3 (z=318). Direction: inferior .. Peak found: z=-5 (correlation = 0.38416574770896966) .. correcting factor: 1.0 Current disc: 4 (z=276). Direction: inferior .. Peak found: z=2 (correlation = 0.36015524526536513) .. correcting factor: 0.981981981981982 Current disc: 5 (z=246). Direction: inferior .. Peak found: z=-3 (correlation = 0.3221388547598374) .. correcting factor: 1.0016380016380015 Current disc: 6 (z=212). Direction: inferior .. Peak found: z=1 (correlation = 0.42965685306863804) .. correcting factor: 0.9948587884071755 Current disc: 7 (z=179). Direction: inferior .. Peak found: z=2 (correlation = 0.3894912033236374) .. correcting factor: 0.9859117354373521 Current disc: 8 (z=139). Direction: inferior .. Peak found: z=3 (correlation = 0.38433477885062817) .. correcting factor: 0.974635308115737 Current disc: 9 (z=97). Direction: inferior .. Peak found: z=2 (correlation = 0.5019980171344993) .. correcting factor: 0.9696537206882264 Current disc: 10 (z=54). Direction: inferior .. Peak found: z=5 (correlation = 0.459571207148563) .. correcting factor: 0.9585327758774572 Current disc: 11 (z=12). Direction: inferior .. Peak found: z=5 (correlation = 0.5735647356894971) .. correcting factor: 0.9483937840039973 Adding top disc based on adjusted template distance: #0 .. approximate distance: 24 Un-straighten labeling... /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i segmentation_straight_labeled.nii -o segmentation_labeled.nii -t warp_straight2curve.nii.gz -r segmentation.nii -n NearestNeighbor # in /private/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-41-55_label-vertebrae_glj_9nxn Cleaning labeled segmentation: removing labeled voxels outside segmentation... Done cleaning. File /private/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-41-55_label-vertebrae_glj_9nxn/segmentation_labeled.nii already exists. Will overwrite it. Label discs... Un-straighten labeled discs... Dilate labels before warping... Creating temporary folder (/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-42-39_apply-transfo-3d-label_romvz5ke) /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-42-39_apply-transfo-3d-label_romvz5ke/dilated_data.nii -o segmentation_labeled_disc.nii -t warp_straight2curve.nii.gz -r segmentation.nii -n NearestNeighbor # in /private/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-41-55_label-vertebrae_glj_9nxn Take the center of mass of each registered dilated labels... File segmentation_labeled_disc.nii already exists. Will overwrite it. Generate output files... File created: /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w/sub-CSM070_ses-spinalcord_T2w_seg_labeled.nii.gz File created: /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w/sub-CSM070_ses-spinalcord_T2w_seg_labeled_discs.nii.gz mv /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-41-55_label-vertebrae_glj_9nxn/straightening.cache /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w/straightening.cache File created: /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w/straightening.cache mv /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-41-55_label-vertebrae_glj_9nxn/warp_curve2straight.nii.gz /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w/warp_curve2straight.nii.gz File created: /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w/warp_curve2straight.nii.gz mv /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-41-55_label-vertebrae_glj_9nxn/warp_straight2curve.nii.gz /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w/warp_straight2curve.nii.gz File created: /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w/warp_straight2curve.nii.gz mv /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-41-55_label-vertebrae_glj_9nxn/straight_ref.nii.gz /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w/straight_ref.nii.gz File created: /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w/straight_ref.nii.gz Remove temporary files... rm -rf /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-41-55_label-vertebrae_glj_9nxn *** Generate Quality Control (QC) html report *** Resample images to NonexNone mm QcImage: layout with Sagittal slice /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/ses-spinalcord/sub-CSM070/ses-spinalcord/T2w/sct_label_vertebrae/2023_11_14_154242.737930/background_img.png Successfully generated the QC results in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/_json/qc_2023_11_14_154242.737930.json To see the results in a browser, type: open /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/index.html Done! To view results, run one of the following commands (depending on your preferred viewer): fsleyes sub-CSM070_ses-spinalcord_T2w.nii.gz -cm greyscale -a 100.0 sub-CSM070_ses-spinalcord_T2w_seg_labeled.nii.gz -cm subcortical -a 50.0 & fslview_deprecated sub-CSM070_ses-spinalcord_T2w.nii.gz -l Greyscale -t 1 sub-CSM070_ses-spinalcord_T2w_seg_labeled.nii.gz -l MGH-Subcortical -t 0.5 & fslview sub-CSM070_ses-spinalcord_T2w.nii.gz -l Greyscale -t 1 sub-CSM070_ses-spinalcord_T2w_seg_labeled.nii.gz -l MGH-Subcortical -t 0.5 & + file_t2_labels=sub-CSM070_ses-spinalcord_T2w_seg_labeled + file_t2_labels_discs=sub-CSM070_ses-spinalcord_T2w_seg_labeled_discs + sct_label_utils -i sub-CSM070_ses-spinalcord_T2w_seg_labeled_discs.nii.gz -keep 1,2,3,4,5,6,7,8,9 -o sub-CSM070_ses-spinalcord_T2w_seg_labeled_discs_1to9.nii.gz -- Spinal Cord Toolbox (6.0) sct_label_utils -i sub-CSM070_ses-spinalcord_T2w_seg_labeled_discs.nii.gz -keep 1,2,3,4,5,6,7,8,9 -o sub-CSM070_ses-spinalcord_T2w_seg_labeled_discs_1to9.nii.gz -- Generating output files... Done! To view results, run one of the following commands (depending on your preferred viewer): fsleyes sub-CSM070_ses-spinalcord_T2w_seg_labeled_discs.nii.gz sub-CSM070_ses-spinalcord_T2w_seg_labeled_discs_1to9.nii.gz & fslview_deprecated sub-CSM070_ses-spinalcord_T2w_seg_labeled_discs.nii.gz sub-CSM070_ses-spinalcord_T2w_seg_labeled_discs_1to9.nii.gz & fslview sub-CSM070_ses-spinalcord_T2w_seg_labeled_discs.nii.gz sub-CSM070_ses-spinalcord_T2w_seg_labeled_discs_1to9.nii.gz & + file_t2_labels_discs=sub-CSM070_ses-spinalcord_T2w_seg_labeled_discs_1to9 + sct_process_segmentation -i sub-CSM070_ses-spinalcord_T2w_seg.nii.gz -vertfile sub-CSM070_ses-spinalcord_T2w_seg_labeled.nii.gz -vert 2:8 -perlevel 1 -o /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/results/t2w_shape_perlevel.csv -append 1 -- Spinal Cord Toolbox (6.0) sct_process_segmentation -i sub-CSM070_ses-spinalcord_T2w_seg.nii.gz -vertfile sub-CSM070_ses-spinalcord_T2w_seg_labeled.nii.gz -vert 2:8 -perlevel 1 -o /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/results/t2w_shape_perlevel.csv -append 1 -- Done! To view results, type: open /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/results/t2w_shape_perlevel.csv + sct_process_segmentation -i sub-CSM070_ses-spinalcord_T2w_seg.nii.gz -o /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/results/t2w_shape_perslice.csv -append 1 -perslice 1 -angle-corr 1 -vert 2:8 -vertfile sub-CSM070_ses-spinalcord_T2w_seg_labeled.nii.gz -- Spinal Cord Toolbox (6.0) sct_process_segmentation -i sub-CSM070_ses-spinalcord_T2w_seg.nii.gz -o /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/results/t2w_shape_perslice.csv -append 1 -perslice 1 -angle-corr 1 -vert 2:8 -vertfile sub-CSM070_ses-spinalcord_T2w_seg_labeled.nii.gz -- Done! To view results, type: open /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/results/t2w_shape_perslice.csv + sct_register_to_template -i sub-CSM070_ses-spinalcord_T2w.nii.gz -s sub-CSM070_ses-spinalcord_T2w_seg.nii.gz -ldisc sub-CSM070_ses-spinalcord_T2w_seg_labeled_discs_1to9.nii.gz -c t2 -qc /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc -qc-subject sub-CSM070/ses-spinalcord -- Spinal Cord Toolbox (6.0) sct_register_to_template -i sub-CSM070_ses-spinalcord_T2w.nii.gz -s sub-CSM070_ses-spinalcord_T2w_seg.nii.gz -ldisc sub-CSM070_ses-spinalcord_T2w_seg_labeled_discs_1to9.nii.gz -c t2 -qc /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc -qc-subject sub-CSM070/ses-spinalcord -- Check template files... OK: /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_t2.nii.gz OK: /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_label_disc.nii.gz OK: /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_cord.nii.gz Check parameters: Data: sub-CSM070_ses-spinalcord_T2w.nii.gz Landmarks: sub-CSM070_ses-spinalcord_T2w_seg_labeled_discs_1to9.nii.gz Segmentation: sub-CSM070_ses-spinalcord_T2w_seg.nii.gz Path template: /Users/fmuhamma/sct_6.0/data/PAM50 Remove temp files: 1 Check input labels... Creating temporary folder (/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-42-57_register-to-template_cg1wvzof) Copying input data to tmp folder and convert to nii... Check if provided labels are available in the template Binarize segmentation Resample data to 1mm isotropic... load data... Done! To view results, run one of the following commands (depending on your preferred viewer): fsleyes data_1mm.nii & fslview_deprecated data_1mm.nii & fslview data_1mm.nii & load data... Done! To view results, run one of the following commands (depending on your preferred viewer): fsleyes seg_bin_1mm.nii.gz & fslview_deprecated seg_bin_1mm.nii.gz & fslview seg_bin_1mm.nii.gz & To avoid intensity overflow due to convertion to +uint8+, intensity will be rescaled to the maximum quantization scale Change orientation of input images to RPI... Straighten the spinal cord using centerline/segmentation... Creating temporary folder (/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-43-00_straighten-spinalcord_29z_56ku) Copy files to tmp folder... Create the straight space and the safe zone Length of spinal cord: 145.12733740198837 Size of spinal cord in z direction: 139.0548876096542 Ratio length/size: 1.0436694451861366 Safe zone boundaries (curved space): [-65.37891215615662, 73.67597545349759] Safe zone boundaries (straight space): [-68.4151370523237, 76.71220034966467] Image header specifies datatype 'uint8', but array is of type 'float32'. Header metadata will be overwritten to use 'float32'. Image header specifies datatype 'uint8', but array is of type 'float32'. Header metadata will be overwritten to use 'float32'. Warping field generated: tmp.curve2straight.nii.gz Warping field generated: tmp.straight2curve.nii.gz File centerline_ref_rpi.nii.gz already exists. Will overwrite it. Apply transformation to input image... /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i data.nii -o tmp.anat_rigid_warp.nii.gz -t tmp.curve2straight.nii.gz -r centerline_ref_rpi.nii.gz -n 'BSpline[3]' # in /private/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-43-00_straighten-spinalcord_29z_56ku Generate output files... mv /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-43-00_straighten-spinalcord_29z_56ku/tmp.curve2straight.nii.gz ./warp_curve2straight.nii.gz File created: ./warp_curve2straight.nii.gz mv /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-43-00_straighten-spinalcord_29z_56ku/tmp.straight2curve.nii.gz ./warp_straight2curve.nii.gz File created: ./warp_straight2curve.nii.gz cp /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-43-00_straighten-spinalcord_29z_56ku/tmp.anat_rigid_warp.nii.gz ./straight_ref.nii.gz mv /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-43-00_straighten-spinalcord_29z_56ku/tmp.anat_rigid_warp.nii.gz /private/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-42-57_register-to-template_cg1wvzof/seg_bin_1mm_rpi_crop_straight.nii.gz File created: /private/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-42-57_register-to-template_cg1wvzof/seg_bin_1mm_rpi_crop_straight.nii.gz Remove temporary files... rm -rf /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-43-00_straighten-spinalcord_29z_56ku /Users/fmuhamma/sct_6.0/bin/isct_ComposeMultiTransform 3 warp_straight2curve.nii.gz -R /private/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-42-57_register-to-template_cg1wvzof/data_1mm_rpi.nii warp_straight2curve.nii.gz # in /private/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-42-57_register-to-template_cg1wvzof cp warp_curve2straight.nii.gz warp_curve2straightAffine.nii.gz Apply transformation... /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /private/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-42-57_register-to-template_cg1wvzof/data_1mm_rpi.nii -o /private/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-42-57_register-to-template_cg1wvzof/data_1mm_rpi_straightAffine.nii -t warp_curve2straightAffine.nii.gz -r template.nii -n 'BSpline[3]' # in /private/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-42-57_register-to-template_cg1wvzof /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /private/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-42-57_register-to-template_cg1wvzof/seg_bin_1mm_rpi_crop.nii.gz -o /private/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-42-57_register-to-template_cg1wvzof/seg_bin_1mm_rpi_crop_straightAffine.nii.gz -t warp_curve2straightAffine.nii.gz -r template.nii -n Linear # in /private/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-42-57_register-to-template_cg1wvzof Image header specifies datatype 'float64', but array is of type ''. Header metadata will be overwritten to use ''. Crop data in template space (for faster processing)... Sub-sample in z-direction (for faster processing)... load data... load data... load data... load data... Register straight spinal cord to template... Creating temporary folder (/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-44-17_register-wrapper_qbvadpn8) Copying input data to tmp folder and convert to nii... -- ESTIMATE TRANSFORMATION FOR STEP #1 Registration parameters: type ........... imseg algo ........... centermassrot slicewise ...... 0 metric ......... MeanSquares 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 ..... pcahog Creating temporary folder (/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-44-17_register-slicewise_g4hs2whf) Copy input data to temp folder... Get image dimensions of destination image... matrix size: 141 x 141 x 80 voxel size: 0.5mm x 0.5mm x 80mm Split input segmentation... Split destination segmentation... Split input image... Split destination image... Switched to method 'hog' for slice: 77 Switched to method 'hog' for slice: 78 Switched to method 'hog' for slice: 79 Generate warping field... --> step1Warp.nii.gz Generate warping field... --> step1InverseWarp.nii.gz Move warping fields... cp step1Warp.nii.gz /private/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-44-17_register-wrapper_qbvadpn8 cp step1InverseWarp.nii.gz /private/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-44-17_register-wrapper_qbvadpn8 rm -rf /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-44-17_register-slicewise_g4hs2whf -- ESTIMATE TRANSFORMATION FOR STEP #2 Apply transformation from previous step /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i src_seg.nii -o src_seg_reg.nii -t warp_forward_1.nii.gz -r dest_seg_RPI.nii -n NearestNeighbor # in /private/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-44-17_register-wrapper_qbvadpn8 Registration parameters: type ........... seg algo ........... bsplinesyn slicewise ...... 0 metric ......... MeanSquares samplStrategy .. None samplPercent ... 0.2 iter ........... 3 smooth ......... 1 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 /Users/fmuhamma/sct_6.0/bin/isct_antsRegistration --dimensionality 3 --transform 'bsplinesyn[0.5,1,3]' --metric 'MeanSquares[dest_seg_RPI_pad.nii,src_seg_reg.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 1mm --restrict-deformation 1x1x0 --output '[step2,src_seg_reg_regStep2.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /private/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-44-17_register-wrapper_qbvadpn8 Concatenate transformations... /Users/fmuhamma/sct_6.0/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_2.nii.gz warp_forward_1.nii.gz # in /private/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-44-17_register-wrapper_qbvadpn8 /Users/fmuhamma/sct_6.0/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii warp_inverse_1.nii.gz warp_inverse_2.nii.gz # in /private/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-44-17_register-wrapper_qbvadpn8 Apply transfo source --> dest... /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i src.nii -o src_reg.nii -t warp_src2dest.nii.gz -r dest.nii -n Linear # in /private/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-44-17_register-wrapper_qbvadpn8 Apply transfo dest --> source... /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i dest.nii -o dest_reg.nii -t warp_dest2src.nii.gz -r src.nii -n Linear # in /private/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-44-17_register-wrapper_qbvadpn8 Generate output files... mv /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-44-17_register-wrapper_qbvadpn8/src_reg.nii data_1mm_rpi_straightAffine_crop_sub_reg.nii File created: data_1mm_rpi_straightAffine_crop_sub_reg.nii mv /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-44-17_register-wrapper_qbvadpn8/warp_src2dest.nii.gz warp_data_1mm_rpi_straightAffine_crop_sub2template_crop_sub.nii.gz File created: warp_data_1mm_rpi_straightAffine_crop_sub2template_crop_sub.nii.gz mv /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-44-17_register-wrapper_qbvadpn8/dest_reg.nii template_crop_sub_reg.nii File created: template_crop_sub_reg.nii mv /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-44-17_register-wrapper_qbvadpn8/warp_dest2src.nii.gz warp_template_crop_sub2data_1mm_rpi_straightAffine_crop_sub.nii.gz File created: warp_template_crop_sub2data_1mm_rpi_straightAffine_crop_sub.nii.gz Remove temporary files... rm -rf /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-44-17_register-wrapper_qbvadpn8 Concatenate transformations: anat --> template... /Users/fmuhamma/sct_6.0/bin/isct_ComposeMultiTransform 3 warp_anat2template.nii.gz -R template.nii warp_data_1mm_rpi_straightAffine_crop_sub2template_crop_sub.nii.gz warp_curve2straightAffine.nii.gz # in /private/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-42-57_register-to-template_cg1wvzof Concatenate transformations: template --> anat... /Users/fmuhamma/sct_6.0/bin/isct_ComposeMultiTransform 3 warp_template2anat.nii.gz -R data.nii warp_straight2curve.nii.gz warp_template_crop_sub2data_1mm_rpi_straightAffine_crop_sub.nii.gz # in /private/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-42-57_register-to-template_cg1wvzof /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i template.nii -o template2anat.nii.gz -t warp_template2anat.nii.gz -r data.nii -n 'BSpline[3]' # in /private/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-42-57_register-to-template_cg1wvzof /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i data.nii -o anat2template.nii.gz -t warp_anat2template.nii.gz -r template.nii -n 'BSpline[3]' # in /private/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-42-57_register-to-template_cg1wvzof Generate output files... mv /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-42-57_register-to-template_cg1wvzof/warp_template2anat.nii.gz warp_template2anat.nii.gz File created: warp_template2anat.nii.gz mv /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-42-57_register-to-template_cg1wvzof/warp_anat2template.nii.gz warp_anat2template.nii.gz File created: warp_anat2template.nii.gz mv /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-42-57_register-to-template_cg1wvzof/template2anat.nii.gz template2anat.nii.gz File created: template2anat.nii.gz mv /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-42-57_register-to-template_cg1wvzof/anat2template.nii.gz anat2template.nii.gz File created: anat2template.nii.gz File straightening.cache already exists. Deleting it.. mv /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-42-57_register-to-template_cg1wvzof/straightening.cache straightening.cache File created: straightening.cache File warp_curve2straight.nii.gz already exists. Deleting it.. mv /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-42-57_register-to-template_cg1wvzof/warp_curve2straight.nii.gz warp_curve2straight.nii.gz File created: warp_curve2straight.nii.gz File warp_straight2curve.nii.gz already exists. Deleting it.. mv /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-42-57_register-to-template_cg1wvzof/warp_straight2curve.nii.gz warp_straight2curve.nii.gz File created: warp_straight2curve.nii.gz File straight_ref.nii.gz already exists. Deleting it.. mv /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-42-57_register-to-template_cg1wvzof/straight_ref.nii.gz straight_ref.nii.gz File created: straight_ref.nii.gz Delete temporary files... rm -rf /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-42-57_register-to-template_cg1wvzof Finished! Elapsed time: 190s *** 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'. QcImage: layout with Axial slice Compute center of mass at each slice /Users/FMUHAMMA/sct_6.0/python/envs/venv_sct/lib/python3.9/site-packages/scipy/ndimage/_measurements.py:1535: RuntimeWarning: invalid value encountered in double_scalars results = [sum(input * grids[dir].astype(float), labels, index) / normalizer /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/ses-spinalcord/sub-CSM070/ses-spinalcord/T2w/sct_register_to_template/2023_11_14_154611.583162/background_img.png Successfully generated the QC results in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/_json/qc_2023_11_14_154611.583162.json To see the results in a browser, type: open /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/index.html Done! To view results, run one of the following commands (depending on your preferred viewer): fsleyes sub-CSM070_ses-spinalcord_T2w.nii.gz template2anat.nii.gz & fslview_deprecated sub-CSM070_ses-spinalcord_T2w.nii.gz template2anat.nii.gz & fslview sub-CSM070_ses-spinalcord_T2w.nii.gz template2anat.nii.gz & Done! To view results, run one of the following commands (depending on your preferred viewer): fsleyes /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_t2.nii.gz anat2template.nii.gz & fslview_deprecated /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_t2.nii.gz anat2template.nii.gz & fslview /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_t2.nii.gz anat2template.nii.gz & + sct_warp_template -d sub-CSM070_ses-spinalcord_T2w.nii.gz -w warp_template2anat.nii.gz -qc /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc -qc-subject sub-CSM070/ses-spinalcord -- Spinal Cord Toolbox (6.0) sct_warp_template -d sub-CSM070_ses-spinalcord_T2w.nii.gz -w warp_template2anat.nii.gz -qc /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc -qc-subject sub-CSM070/ses-spinalcord -- Check parameters: Working directory ........ /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w Destination image ........ sub-CSM070_ses-spinalcord_T2w.nii.gz Warping field ............ warp_template2anat.nii.gz Path template ............ /Users/fmuhamma/sct_6.0/data/PAM50 Output folder ............ label WARP TEMPLATE: /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_t1.nii.gz -o label/template/PAM50_t1.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_t2.nii.gz -o label/template/PAM50_t2.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_t2s.nii.gz -o label/template/PAM50_t2s.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_cord.nii.gz -o label/template/PAM50_cord.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n NearestNeighbor # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_wm.nii.gz -o label/template/PAM50_wm.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_gm.nii.gz -o label/template/PAM50_gm.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_csf.nii.gz -o label/template/PAM50_csf.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n NearestNeighbor # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz -o label/template/PAM50_levels.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n NearestNeighbor # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels_continuous.nii.gz -o label/template/PAM50_levels_continuous.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_label_body.nii.gz -o label/template/PAM50_label_body.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_label_disc.nii.gz -o label/template/PAM50_label_disc.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_label_discPosterior.nii.gz -o label/template/PAM50_label_discPosterior.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_spine.nii.gz -o label/template/PAM50_spine.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_centerline.nii.gz -o label/template/PAM50_centerline.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_label_spinal_levels.nii.gz -o label/template/PAM50_label_spinal_levels.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n NearestNeighbor # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w cp /Users/fmuhamma/sct_6.0/data/PAM50/template/info_label.txt label/template WARP ATLAS OF WHITE MATTER TRACTS: /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_00.nii.gz -o label/atlas/PAM50_atlas_00.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_01.nii.gz -o label/atlas/PAM50_atlas_01.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_02.nii.gz -o label/atlas/PAM50_atlas_02.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_03.nii.gz -o label/atlas/PAM50_atlas_03.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_04.nii.gz -o label/atlas/PAM50_atlas_04.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_05.nii.gz -o label/atlas/PAM50_atlas_05.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_06.nii.gz -o label/atlas/PAM50_atlas_06.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_07.nii.gz -o label/atlas/PAM50_atlas_07.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_08.nii.gz -o label/atlas/PAM50_atlas_08.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_09.nii.gz -o label/atlas/PAM50_atlas_09.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_10.nii.gz -o label/atlas/PAM50_atlas_10.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_11.nii.gz -o label/atlas/PAM50_atlas_11.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_12.nii.gz -o label/atlas/PAM50_atlas_12.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_13.nii.gz -o label/atlas/PAM50_atlas_13.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_14.nii.gz -o label/atlas/PAM50_atlas_14.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_15.nii.gz -o label/atlas/PAM50_atlas_15.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_16.nii.gz -o label/atlas/PAM50_atlas_16.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_17.nii.gz -o label/atlas/PAM50_atlas_17.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_18.nii.gz -o label/atlas/PAM50_atlas_18.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_19.nii.gz -o label/atlas/PAM50_atlas_19.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_20.nii.gz -o label/atlas/PAM50_atlas_20.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_21.nii.gz -o label/atlas/PAM50_atlas_21.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_22.nii.gz -o label/atlas/PAM50_atlas_22.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_23.nii.gz -o label/atlas/PAM50_atlas_23.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_24.nii.gz -o label/atlas/PAM50_atlas_24.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_25.nii.gz -o label/atlas/PAM50_atlas_25.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_26.nii.gz -o label/atlas/PAM50_atlas_26.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_27.nii.gz -o label/atlas/PAM50_atlas_27.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_28.nii.gz -o label/atlas/PAM50_atlas_28.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_29.nii.gz -o label/atlas/PAM50_atlas_29.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_30.nii.gz -o label/atlas/PAM50_atlas_30.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_31.nii.gz -o label/atlas/PAM50_atlas_31.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_32.nii.gz -o label/atlas/PAM50_atlas_32.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_33.nii.gz -o label/atlas/PAM50_atlas_33.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_34.nii.gz -o label/atlas/PAM50_atlas_34.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_35.nii.gz -o label/atlas/PAM50_atlas_35.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_36.nii.gz -o label/atlas/PAM50_atlas_36.nii.gz -t warp_template2anat.nii.gz -r sub-CSM070_ses-spinalcord_T2w.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w cp /Users/fmuhamma/sct_6.0/data/PAM50/atlas/info_label.txt label/atlas *** Generate Quality Control (QC) html report *** Resample images to 0.6x0.6 mm QcImage: layout with Axial slice Compute center of mass at each slice /Users/FMUHAMMA/sct_6.0/python/envs/venv_sct/lib/python3.9/site-packages/scipy/ndimage/_measurements.py:1535: RuntimeWarning: invalid value encountered in double_scalars results = [sum(input * grids[dir].astype(float), labels, index) / normalizer /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/ses-spinalcord/sub-CSM070/ses-spinalcord/T2w/sct_warp_template/2023_11_14_154740.375581/background_img.png Successfully generated the QC results in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/_json/qc_2023_11_14_154740.375581.json To see the results in a browser, type: open /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/index.html Done! To view results, run one of the following commands (depending on your preferred viewer): fsleyes sub-CSM070_ses-spinalcord_T2w.nii.gz -cm greyscale -a 100.0 label/template/PAM50_t2.nii.gz -cm greyscale -dr 0 4000 -a 100.0 label/template/PAM50_gm.nii.gz -cm red-yellow -dr 0.4 1 -a 50.0 label/template/PAM50_wm.nii.gz -cm blue-lightblue -dr 0.4 1 -a 50.0 & fslview_deprecated sub-CSM070_ses-spinalcord_T2w.nii.gz -l Greyscale -t 1 label/template/PAM50_t2.nii.gz -l Greyscale -b 0,4000 -t 1 label/template/PAM50_gm.nii.gz -l Red-Yellow -b 0.4,1 -t 0.5 label/template/PAM50_wm.nii.gz -l Blue-Lightblue -b 0.4,1 -t 0.5 & fslview sub-CSM070_ses-spinalcord_T2w.nii.gz -l Greyscale -t 1 label/template/PAM50_t2.nii.gz -l Greyscale -b 0,4000 -t 1 label/template/PAM50_gm.nii.gz -l Red-Yellow -b 0.4,1 -t 0.5 label/template/PAM50_wm.nii.gz -l Blue-Lightblue -b 0.4,1 -t 0.5 & + sct_detect_pmj -i sub-CSM070_ses-spinalcord_T2w.nii.gz -c t2 -qc /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc -qc-subject sub-CSM070/ses-spinalcord -- Spinal Cord Toolbox (6.0) sct_detect_pmj -i sub-CSM070_ses-spinalcord_T2w.nii.gz -c t2 -qc /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc -qc-subject sub-CSM070/ses-spinalcord -- Creating temporary folder (/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-47-41_detect-pmj_8z0f81ir) cp sub-CSM070_ses-spinalcord_T2w.nii.gz /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-47-41_detect-pmj_8z0f81ir Bounding box: x=[0, 320], y=[0, 320], z=[28, 30] Cropping the image... Run PMJ detector ['isct_spine_detect', '/Users/fmuhamma/sct_6.0/data/pmj_models/t2_model', 'sub-CSM070_ses-spinalcord_T2w_midSag', 'sub-CSM070_ses-spinalcord_T2w_map_pmj'] Ponto-Medullary Junction detected .. Peak found: x=-2 (correlation = 0.6125799742049196) R-L coordinate adjusted from 28 to 26) Bounding box: x=[0, 320], y=[0, 320], z=[26, 28] Cropping the image... File sub-CSM070_ses-spinalcord_T2w_midSag.nii already exists. Will overwrite it. Run PMJ detector ['isct_spine_detect', '/Users/fmuhamma/sct_6.0/data/pmj_models/t2_model', 'sub-CSM070_ses-spinalcord_T2w_midSag', 'sub-CSM070_ses-spinalcord_T2w_map_pmj.nii'] Ponto-Medullary Junction detected x_pmj = 137 y_pmj = 47 z_pmj = 26 Save resulting file... cp /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-47-41_detect-pmj_8z0f81ir/sub-CSM070_ses-spinalcord_T2w_pmj.nii.gz /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w/sub-CSM070_ses-spinalcord_T2w_pmj.nii.gz rm -rf /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-47-41_detect-pmj_8z0f81ir *** Generate Quality Control (QC) html report *** Resample images to NonexNone mm QcImage: layout with Sagittal slice /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/ses-spinalcord/sub-CSM070/ses-spinalcord/T2w/sct_detect_pmj/2023_11_14_154743.389561/background_img.png Successfully generated the QC results in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/_json/qc_2023_11_14_154743.389561.json To see the results in a browser, type: open /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/index.html Done! To view results, run one of the following commands (depending on your preferred viewer): fsleyes sub-CSM070_ses-spinalcord_T2w.nii.gz -cm greyscale sub-CSM070_ses-spinalcord_T2w_pmj.nii.gz -cm red & fslview_deprecated sub-CSM070_ses-spinalcord_T2w.nii.gz -l Greyscale sub-CSM070_ses-spinalcord_T2w_pmj.nii.gz -l Red & fslview sub-CSM070_ses-spinalcord_T2w.nii.gz -l Greyscale sub-CSM070_ses-spinalcord_T2w_pmj.nii.gz -l Red & + sct_process_segmentation -i sub-CSM070_ses-spinalcord_T2w_seg.nii.gz -pmj sub-CSM070_ses-spinalcord_T2w_pmj.nii.gz -pmj-distance 60 -pmj-extent 30 -qc /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc -qc-subject sub-CSM070/ses-spinalcord -qc-image sub-CSM070_ses-spinalcord_T2w.nii.gz -o csa_pmj.csv -- Spinal Cord Toolbox (6.0) sct_process_segmentation -i sub-CSM070_ses-spinalcord_T2w_seg.nii.gz -pmj sub-CSM070_ses-spinalcord_T2w_pmj.nii.gz -pmj-distance 60 -pmj-extent 30 -qc /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc -qc-subject sub-CSM070/ses-spinalcord -qc-image sub-CSM070_ses-spinalcord_T2w.nii.gz -o csa_pmj.csv -- Image header specifies datatype 'uint8', but array is of type 'int16'. Header metadata will be overwritten to use 'int16'. Image header specifies datatype 'uint8', but array is of type 'int16'. Header metadata will be overwritten to use 'int16'. Creating temporary folder (/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-47-47_pmj-qc_302sbni8) Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'. *** Generate Quality Control (QC) html report *** Resample images to NonexNone mm QcImage: layout with Sagittal slice /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/ses-spinalcord/sub-CSM070/ses-spinalcord/T2w/sct_process_segmentation/2023_11_14_154748.226430/background_img.png Successfully generated the QC results in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/_json/qc_2023_11_14_154748.226430.json To see the results in a browser, type: open /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/index.html Done! To view results, type: open /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w/csa_pmj.csv + sct_process_segmentation -i sub-CSM070_ses-spinalcord_T2w_seg.nii.gz -vertfile sub-CSM070_ses-spinalcord_T2w_seg_labeled.nii.gz -perslice 1 -normalize-PAM50 1 -v 2 -o t2w_shape_PAM50.csv -append 1 -- Spinal Cord Toolbox (6.0) sct_process_segmentation -i sub-CSM070_ses-spinalcord_T2w_seg.nii.gz -vertfile sub-CSM070_ses-spinalcord_T2w_seg_labeled.nii.gz -perslice 1 -normalize-PAM50 1 -v 2 -o t2w_shape_PAM50.csv -append 1 -- Loaded /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w/sub-CSM070_ses-spinalcord_T2w_seg.nii.gz orientation ASR shape (320, 320, 56) Affine matrix: [[-7.97595024e-01 0.00000000e+00 -6.19839989e-02 3.41326942e+01] [ 0.00000000e+00 8.00000012e-01 0.00000000e+00 -9.15000076e+01] [-6.19839989e-02 0.00000000e+00 7.97595024e-01 -1.18311813e+02] [ 0.00000000e+00 0.00000000e+00 0.00000000e+00 1.00000000e+00]] Smoothing factor: smooth=7.999998927116394 Smoothing factor: smooth=7.999998927116394 Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded sub-CSM070_ses-spinalcord_T2w_seg_labeled.nii.gz (/Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w/sub-CSM070_ses-spinalcord_T2w_seg_labeled.nii.gz) orientation ASR shape (320, 320, 56) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Done! To view results, type: open /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w/t2w_shape_PAM50.csv + sct_maths -i label/atlas/PAM50_atlas_00.nii.gz -add label/atlas/PAM50_atlas_02.nii.gz label/atlas/PAM50_atlas_04.nii.gz label/atlas/PAM50_atlas_06.nii.gz label/atlas/PAM50_atlas_08.nii.gz label/atlas/PAM50_atlas_10.nii.gz label/atlas/PAM50_atlas_12.nii.gz label/atlas/PAM50_atlas_14.nii.gz label/atlas/PAM50_atlas_16.nii.gz label/atlas/PAM50_atlas_18.nii.gz label/atlas/PAM50_atlas_20.nii.gz label/atlas/PAM50_atlas_22.nii.gz label/atlas/PAM50_atlas_24.nii.gz label/atlas/PAM50_atlas_26.nii.gz label/atlas/PAM50_atlas_28.nii.gz label/atlas/PAM50_atlas_30.nii.gz label/atlas/PAM50_atlas_32.nii.gz label/atlas/PAM50_atlas_34.nii.gz -o PAM50_atlas_left_hemi_cord.nii.gz -- Spinal Cord Toolbox (6.0) sct_maths -i label/atlas/PAM50_atlas_00.nii.gz -add label/atlas/PAM50_atlas_02.nii.gz label/atlas/PAM50_atlas_04.nii.gz label/atlas/PAM50_atlas_06.nii.gz label/atlas/PAM50_atlas_08.nii.gz label/atlas/PAM50_atlas_10.nii.gz label/atlas/PAM50_atlas_12.nii.gz label/atlas/PAM50_atlas_14.nii.gz label/atlas/PAM50_atlas_16.nii.gz label/atlas/PAM50_atlas_18.nii.gz label/atlas/PAM50_atlas_20.nii.gz label/atlas/PAM50_atlas_22.nii.gz label/atlas/PAM50_atlas_24.nii.gz label/atlas/PAM50_atlas_26.nii.gz label/atlas/PAM50_atlas_28.nii.gz label/atlas/PAM50_atlas_30.nii.gz label/atlas/PAM50_atlas_32.nii.gz label/atlas/PAM50_atlas_34.nii.gz -o PAM50_atlas_left_hemi_cord.nii.gz -- Done! To view results, run one of the following commands (depending on your preferred viewer): fsleyes PAM50_atlas_left_hemi_cord.nii.gz & fslview_deprecated PAM50_atlas_left_hemi_cord.nii.gz & fslview PAM50_atlas_left_hemi_cord.nii.gz & + sct_maths -i label/atlas/PAM50_atlas_01.nii.gz -add label/atlas/PAM50_atlas_03.nii.gz label/atlas/PAM50_atlas_05.nii.gz label/atlas/PAM50_atlas_07.nii.gz label/atlas/PAM50_atlas_09.nii.gz label/atlas/PAM50_atlas_11.nii.gz label/atlas/PAM50_atlas_13.nii.gz label/atlas/PAM50_atlas_15.nii.gz label/atlas/PAM50_atlas_17.nii.gz label/atlas/PAM50_atlas_19.nii.gz label/atlas/PAM50_atlas_21.nii.gz label/atlas/PAM50_atlas_23.nii.gz label/atlas/PAM50_atlas_25.nii.gz label/atlas/PAM50_atlas_27.nii.gz label/atlas/PAM50_atlas_29.nii.gz label/atlas/PAM50_atlas_31.nii.gz label/atlas/PAM50_atlas_33.nii.gz label/atlas/PAM50_atlas_35.nii.gz -o PAM50_atlas_right_hemi_cord.nii.gz -- Spinal Cord Toolbox (6.0) sct_maths -i label/atlas/PAM50_atlas_01.nii.gz -add label/atlas/PAM50_atlas_03.nii.gz label/atlas/PAM50_atlas_05.nii.gz label/atlas/PAM50_atlas_07.nii.gz label/atlas/PAM50_atlas_09.nii.gz label/atlas/PAM50_atlas_11.nii.gz label/atlas/PAM50_atlas_13.nii.gz label/atlas/PAM50_atlas_15.nii.gz label/atlas/PAM50_atlas_17.nii.gz label/atlas/PAM50_atlas_19.nii.gz label/atlas/PAM50_atlas_21.nii.gz label/atlas/PAM50_atlas_23.nii.gz label/atlas/PAM50_atlas_25.nii.gz label/atlas/PAM50_atlas_27.nii.gz label/atlas/PAM50_atlas_29.nii.gz label/atlas/PAM50_atlas_31.nii.gz label/atlas/PAM50_atlas_33.nii.gz label/atlas/PAM50_atlas_35.nii.gz -o PAM50_atlas_right_hemi_cord.nii.gz -- Done! To view results, run one of the following commands (depending on your preferred viewer): fsleyes PAM50_atlas_right_hemi_cord.nii.gz & fslview_deprecated PAM50_atlas_right_hemi_cord.nii.gz & fslview PAM50_atlas_right_hemi_cord.nii.gz & + sct_maths -i PAM50_atlas_right_hemi_cord.nii.gz -bin 0.5 -o PAM50_atlas_right_hemi_cord_bin.nii.gz -- Spinal Cord Toolbox (6.0) sct_maths -i PAM50_atlas_right_hemi_cord.nii.gz -bin 0.5 -o PAM50_atlas_right_hemi_cord_bin.nii.gz -- Image header specifies datatype 'float64', but array is of type ''. Header metadata will be overwritten to use ''. Done! To view results, run one of the following commands (depending on your preferred viewer): fsleyes PAM50_atlas_right_hemi_cord_bin.nii.gz & fslview_deprecated PAM50_atlas_right_hemi_cord_bin.nii.gz & fslview PAM50_atlas_right_hemi_cord_bin.nii.gz & + sct_maths -i PAM50_atlas_left_hemi_cord.nii.gz -bin 0.5 -o PAM50_atlas_left_hemi_cord_bin.nii.gz -- Spinal Cord Toolbox (6.0) sct_maths -i PAM50_atlas_left_hemi_cord.nii.gz -bin 0.5 -o PAM50_atlas_left_hemi_cord_bin.nii.gz -- Image header specifies datatype 'float64', but array is of type ''. Header metadata will be overwritten to use ''. Done! To view results, run one of the following commands (depending on your preferred viewer): fsleyes PAM50_atlas_left_hemi_cord_bin.nii.gz & fslview_deprecated PAM50_atlas_left_hemi_cord_bin.nii.gz & fslview PAM50_atlas_left_hemi_cord_bin.nii.gz & + python3 /Users/FMUHAMMA/Desktop/Mri/create_right_left_seg_mask.py -seg sub-CSM070_ses-spinalcord_T2w_seg.nii.gz -PAM50-R PAM50_atlas_right_hemi_cord_bin.nii.gz -PAM50-L PAM50_atlas_left_hemi_cord_bin.nii.gz + sct_process_segmentation -i sub-CSM070_ses-spinalcord_T2w_seg_right.nii.gz -vertfile sub-CSM070_ses-spinalcord_T2w_seg_labeled.nii.gz -vert 2:8 -perlevel 1 -o /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/results/t2w_shape_right_perlevel.csv -append 1 -- Spinal Cord Toolbox (6.0) sct_process_segmentation -i sub-CSM070_ses-spinalcord_T2w_seg_right.nii.gz -vertfile sub-CSM070_ses-spinalcord_T2w_seg_labeled.nii.gz -vert 2:8 -perlevel 1 -o /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/results/t2w_shape_right_perlevel.csv -append 1 -- Done! To view results, type: open /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/results/t2w_shape_right_perlevel.csv + sct_process_segmentation -i sub-CSM070_ses-spinalcord_T2w_seg_right.nii.gz -vertfile sub-CSM070_ses-spinalcord_T2w_seg_labeled.nii.gz -perslice 1 -normalize-PAM50 1 -v 2 -o /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/results/t2w_shape_right_PAM50.csv -append 1 -- Spinal Cord Toolbox (6.0) sct_process_segmentation -i sub-CSM070_ses-spinalcord_T2w_seg_right.nii.gz -vertfile sub-CSM070_ses-spinalcord_T2w_seg_labeled.nii.gz -perslice 1 -normalize-PAM50 1 -v 2 -o /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/results/t2w_shape_right_PAM50.csv -append 1 -- Loaded /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w/sub-CSM070_ses-spinalcord_T2w_seg_right.nii.gz orientation ASR shape (320, 320, 56) Affine matrix: [[-7.97595024e-01 0.00000000e+00 -6.19839989e-02 3.41326942e+01] [ 0.00000000e+00 8.00000012e-01 0.00000000e+00 -9.15000076e+01] [-6.19839989e-02 0.00000000e+00 7.97595024e-01 -1.18311813e+02] [ 0.00000000e+00 0.00000000e+00 0.00000000e+00 1.00000000e+00]] Smoothing factor: smooth=7.999998927116394 Smoothing factor: smooth=7.999998927116394 Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded sub-CSM070_ses-spinalcord_T2w_seg_labeled.nii.gz (/Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w/sub-CSM070_ses-spinalcord_T2w_seg_labeled.nii.gz) orientation ASR shape (320, 320, 56) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Done! To view results, type: open /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/results/t2w_shape_right_PAM50.csv + sct_process_segmentation -i sub-CSM070_ses-spinalcord_T2w_seg_left.nii.gz -vertfile sub-CSM070_ses-spinalcord_T2w_seg_labeled.nii.gz -vert 2:8 -perlevel 1 -o /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/results/t2w_shape_left_perlevel.csv -append 1 -- Spinal Cord Toolbox (6.0) sct_process_segmentation -i sub-CSM070_ses-spinalcord_T2w_seg_left.nii.gz -vertfile sub-CSM070_ses-spinalcord_T2w_seg_labeled.nii.gz -vert 2:8 -perlevel 1 -o /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/results/t2w_shape_left_perlevel.csv -append 1 -- Done! To view results, type: open /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/results/t2w_shape_left_perlevel.csv + sct_process_segmentation -i sub-CSM070_ses-spinalcord_T2w_seg_left.nii.gz -vertfile sub-CSM070_ses-spinalcord_T2w_seg_labeled.nii.gz -perslice 1 -normalize-PAM50 1 -v 2 -o /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/results/t2w_shape_left_PAM50.csv -append 1 -- Spinal Cord Toolbox (6.0) sct_process_segmentation -i sub-CSM070_ses-spinalcord_T2w_seg_left.nii.gz -vertfile sub-CSM070_ses-spinalcord_T2w_seg_labeled.nii.gz -perslice 1 -normalize-PAM50 1 -v 2 -o /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/results/t2w_shape_left_PAM50.csv -append 1 -- Loaded /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w/sub-CSM070_ses-spinalcord_T2w_seg_left.nii.gz orientation ASR shape (320, 320, 56) Affine matrix: [[-7.97595024e-01 0.00000000e+00 -6.19839989e-02 3.41326942e+01] [ 0.00000000e+00 8.00000012e-01 0.00000000e+00 -9.15000076e+01] [-6.19839989e-02 0.00000000e+00 7.97595024e-01 -1.18311813e+02] [ 0.00000000e+00 0.00000000e+00 0.00000000e+00 1.00000000e+00]] Smoothing factor: smooth=7.999998927116394 Smoothing factor: smooth=7.999998927116394 Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded sub-CSM070_ses-spinalcord_T2w_seg_labeled.nii.gz (/Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w/sub-CSM070_ses-spinalcord_T2w_seg_labeled.nii.gz) orientation ASR shape (320, 320, 56) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Loaded /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz orientation RPI shape (141, 141, 991) Done! To view results, type: open /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/results/t2w_shape_left_PAM50.csv + cd .. + file_t2star=sub-CSM070_ses-spinalcord_T2star + [[ -f sub-CSM070_ses-spinalcord_T2star.nii.gz ]] + mkdir -p /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star + cp sub-CSM070_ses-spinalcord_T2star.nii.gz /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star + cd T2star + segment_if_does_not_exist sub-CSM070_ses-spinalcord_T2star t2s deepseg anat + local file=sub-CSM070_ses-spinalcord_T2star + local contrast=t2s + local segmentation_method=deepseg + local subfolder=anat + FILESEG=sub-CSM070_ses-spinalcord_T2star_seg + FILESEGMANUAL=/Users/fmuhamma/Desktop/Mri/BIDS/derivatives/labels/sub-CSM070/ses-spinalcord/ses-spinalcord/anat/sub-CSM070_ses-spinalcord_T2star_seg.nii.gz + echo + echo 'Looking for manual segmentation: /Users/fmuhamma/Desktop/Mri/BIDS/derivatives/labels/sub-CSM070/ses-spinalcord/ses-spinalcord/anat/sub-CSM070_ses-spinalcord_T2star_seg.nii.gz' Looking for manual segmentation: /Users/fmuhamma/Desktop/Mri/BIDS/derivatives/labels/sub-CSM070/ses-spinalcord/ses-spinalcord/anat/sub-CSM070_ses-spinalcord_T2star_seg.nii.gz + [[ -e /Users/fmuhamma/Desktop/Mri/BIDS/derivatives/labels/sub-CSM070/ses-spinalcord/ses-spinalcord/anat/sub-CSM070_ses-spinalcord_T2star_seg.nii.gz ]] + echo 'Not found. Proceeding with automatic segmentation.' Not found. Proceeding with automatic segmentation. + [[ deepseg == \d\e\e\p\s\e\g ]] + sct_deepseg_sc -i sub-CSM070_ses-spinalcord_T2star.nii.gz -c t2s -qc /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc -qc-subject sub-CSM070/ses-spinalcord -- Spinal Cord Toolbox (6.0) sct_deepseg_sc -i sub-CSM070_ses-spinalcord_T2star.nii.gz -c t2s -qc /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc -qc-subject sub-CSM070/ses-spinalcord -- Config deepseg_sc: Centerline algorithm: svm Brain in image: False Kernel dimension: 2d Contrast: t2s Threshold: 0.89 Creating temporary folder (/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-49-51_deepseg-sc_027y02hi) Reorient the image to RPI, if necessary... Finding the spinal cord centerline... Creating temporary folder (/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-49-51_optic-detect-centerline_6nwc2r7g) Remove temporary files... rm -rf /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-49-51_optic-detect-centerline_6nwc2r7g 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'. Remove temporary files... rm -rf /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-49-51_deepseg-sc_027y02hi *** 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'. QcImage: layout with Axial slice Compute center of mass at each slice /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/ses-spinalcord/sub-CSM070/ses-spinalcord/T2star/sct_deepseg_sc/2023_11_14_154954.649827/background_img.png Successfully generated the QC results in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/_json/qc_2023_11_14_154954.649827.json To see the results in a browser, type: open /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/index.html Done! To view results, run one of the following commands (depending on your preferred viewer): fsleyes sub-CSM070_ses-spinalcord_T2star.nii.gz -cm greyscale sub-CSM070_ses-spinalcord_T2star_seg.nii.gz -cm red -a 70.0 & fslview_deprecated sub-CSM070_ses-spinalcord_T2star.nii.gz -l Greyscale sub-CSM070_ses-spinalcord_T2star_seg.nii.gz -l Red -t 0.7 & fslview sub-CSM070_ses-spinalcord_T2star.nii.gz -l Greyscale sub-CSM070_ses-spinalcord_T2star_seg.nii.gz -l Red -t 0.7 & + file_t2star_seg=sub-CSM070_ses-spinalcord_T2star_seg + segment_gm_if_does_not_exist sub-CSM070_ses-spinalcord_T2star + local file=sub-CSM070_ses-spinalcord_T2star + FILESEG=sub-CSM070_ses-spinalcord_T2star_gmseg + FILESEGMANUAL=/Users/fmuhamma/Desktop/Mri/BIDS/derivatives/labels/sub-CSM070/ses-spinalcord/anat/sub-CSM070_ses-spinalcord_T2star_gmseg.nii.gz + echo 'Looking for manual segmentation: /Users/fmuhamma/Desktop/Mri/BIDS/derivatives/labels/sub-CSM070/ses-spinalcord/anat/sub-CSM070_ses-spinalcord_T2star_gmseg.nii.gz' Looking for manual segmentation: /Users/fmuhamma/Desktop/Mri/BIDS/derivatives/labels/sub-CSM070/ses-spinalcord/anat/sub-CSM070_ses-spinalcord_T2star_gmseg.nii.gz + [[ -e /Users/fmuhamma/Desktop/Mri/BIDS/derivatives/labels/sub-CSM070/ses-spinalcord/anat/sub-CSM070_ses-spinalcord_T2star_gmseg.nii.gz ]] + echo 'Not found. Proceeding with automatic segmentation.' Not found. Proceeding with automatic segmentation. + sct_deepseg_gm -i sub-CSM070_ses-spinalcord_T2star.nii.gz -qc /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc -qc-subject sub-CSM070/ses-spinalcord -- Spinal Cord Toolbox (6.0) sct_deepseg_gm -i sub-CSM070_ses-spinalcord_T2star.nii.gz -qc /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc -qc-subject sub-CSM070/ses-spinalcord -- *** Generate Quality Control (QC) html report *** Resample images to 0.6x0.6 mm Image header specifies datatype 'int16', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'. QcImage: layout with Axial slice Compute center of mass at each slice /Users/FMUHAMMA/sct_6.0/python/envs/venv_sct/lib/python3.9/site-packages/scipy/ndimage/_measurements.py:1535: RuntimeWarning: invalid value encountered in double_scalars results = [sum(input * grids[dir].astype(float), labels, index) / normalizer /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/ses-spinalcord/sub-CSM070/ses-spinalcord/T2star/sct_deepseg_gm/2023_11_14_155000.837180/background_img.png Successfully generated the QC results in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/_json/qc_2023_11_14_155000.837180.json To see the results in a browser, type: open /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/index.html Done! To view results, run one of the following commands (depending on your preferred viewer): fsleyes sub-CSM070_ses-spinalcord_T2star.nii.gz -cm greyscale -a 100.0 sub-CSM070_ses-spinalcord_T2star_gmseg.nii.gz -cm red -a 70.0 & fslview_deprecated sub-CSM070_ses-spinalcord_T2star.nii.gz -l Greyscale -t 1 sub-CSM070_ses-spinalcord_T2star_gmseg.nii.gz -l Red -t 0.7 & fslview sub-CSM070_ses-spinalcord_T2star.nii.gz -l Greyscale -t 1 sub-CSM070_ses-spinalcord_T2star_gmseg.nii.gz -l Red -t 0.7 & + file_t2star_gmseg=sub-CSM070_ses-spinalcord_T2star_gmseg + sct_maths -i sub-CSM070_ses-spinalcord_T2star_seg.nii.gz -sub sub-CSM070_ses-spinalcord_T2star_gmseg.nii.gz -o sub-CSM070_ses-spinalcord_T2star_wmseg.nii.gz -- Spinal Cord Toolbox (6.0) sct_maths -i sub-CSM070_ses-spinalcord_T2star_seg.nii.gz -sub sub-CSM070_ses-spinalcord_T2star_gmseg.nii.gz -o sub-CSM070_ses-spinalcord_T2star_wmseg.nii.gz -- Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'. Done! To view results, run one of the following commands (depending on your preferred viewer): fsleyes sub-CSM070_ses-spinalcord_T2star_wmseg.nii.gz & fslview_deprecated sub-CSM070_ses-spinalcord_T2star_wmseg.nii.gz & fslview sub-CSM070_ses-spinalcord_T2star_wmseg.nii.gz & + file_t2star_wmseg=sub-CSM070_ses-spinalcord_T2star_wmseg + sct_register_multimodal -i /Users/FMUHAMMA/sct_6.0/data/PAM50/template/PAM50_t2s.nii.gz -iseg /Users/FMUHAMMA/sct_6.0/data/PAM50/template/PAM50_wm.nii.gz -d sub-CSM070_ses-spinalcord_T2star.nii.gz -dseg sub-CSM070_ses-spinalcord_T2star_wmseg.nii.gz -param step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=10:step=3,type=im,algo=syn,slicewise=1,iter=1,metric=CC -initwarp ../T2w/warp_template2anat.nii.gz -initwarpinv ../T2w/warp_anat2template.nii.gz -qc /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc -qc-subject sub-CSM070/ses-spinalcord -- Spinal Cord Toolbox (6.0) sct_register_multimodal -i /Users/FMUHAMMA/sct_6.0/data/PAM50/template/PAM50_t2s.nii.gz -iseg /Users/FMUHAMMA/sct_6.0/data/PAM50/template/PAM50_wm.nii.gz -d sub-CSM070_ses-spinalcord_T2star.nii.gz -dseg sub-CSM070_ses-spinalcord_T2star_wmseg.nii.gz -param step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=10:step=3,type=im,algo=syn,slicewise=1,iter=1,metric=CC -initwarp ../T2w/warp_template2anat.nii.gz -initwarpinv ../T2w/warp_anat2template.nii.gz -qc /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc -qc-subject sub-CSM070/ses-spinalcord -- Input parameters: Source .............. /Users/FMUHAMMA/sct_6.0/data/PAM50/template/PAM50_t2s.nii.gz (141, 141, 991) Destination ......... sub-CSM070_ses-spinalcord_T2star.nii.gz (448, 448, 20) Init transfo ........ /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w/warp_template2anat.nii.gz Mask ................ Output name ......... Remove temp files ... 1 Verbose ............. 1 Check if input data are 3D... Creating temporary folder (/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-50-04_register-wrapper_vlck6skr) Copying input data to tmp folder and convert to nii... Skip step=0 and replace with initial transformations: /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w/warp_template2anat.nii.gz -- ESTIMATE TRANSFORMATION FOR STEP #1 Apply transformation from previous step /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i src_seg.nii -o src_seg_reg.nii -t /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w/warp_template2anat.nii.gz -r dest_seg_RPI.nii -n NearestNeighbor # in /private/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-50-04_register-wrapper_vlck6skr Registration parameters: type ........... seg algo ........... centermass slicewise ...... 0 metric ......... MeanSquares 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 (/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-50-06_register-slicewise_3w_7tvz4) Copy input data to temp folder... Get image dimensions of destination image... matrix size: 448 x 448 x 20 voxel size: 0.5mm x 0.49999994mm x 20mm Split input segmentation... Split destination segmentation... /Users/fmuhamma/sct_6.0/spinalcordtoolbox/registration/algorithms.py:1443: RuntimeWarning: invalid value encountered in divide coordsrc /= coordsrc.std() Slice #5 is empty. It will be ignored. Generate warping field... --> step1Warp.nii.gz Generate warping field... --> step1InverseWarp.nii.gz Move warping fields... cp step1Warp.nii.gz /private/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-50-04_register-wrapper_vlck6skr cp step1InverseWarp.nii.gz /private/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-50-04_register-wrapper_vlck6skr rm -rf /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-50-06_register-slicewise_3w_7tvz4 -- ESTIMATE TRANSFORMATION FOR STEP #2 Apply transformation from previous step /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i src_seg.nii -o src_seg_reg.nii -t warp_forward_1.nii.gz /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w/warp_template2anat.nii.gz -r dest_seg_RPI.nii -n NearestNeighbor # in /private/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-50-04_register-wrapper_vlck6skr Registration parameters: type ........... seg algo ........... bsplinesyn slicewise ...... 1 metric ......... MeanSquares 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 (/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-50-19_register-slicewise_deazw4tl) Copy input data to temp folder... Get image dimensions of destination image... matrix size: 448 x 448 x 20 voxel size: 0.5mm x 0.49999994mm x 20mm Split input volume... Split destination volume... Merge warping fields along z... Move warping fields... cp step2Warp.nii.gz /private/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-50-04_register-wrapper_vlck6skr cp step2InverseWarp.nii.gz /private/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-50-04_register-wrapper_vlck6skr rm -rf /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-50-19_register-slicewise_deazw4tl -- ESTIMATE TRANSFORMATION FOR STEP #3 Apply transformation from previous step /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i src.nii -o src_reg.nii -t warp_forward_2.nii.gz warp_forward_1.nii.gz /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w/warp_template2anat.nii.gz -r dest_RPI.nii -n 'BSpline[3]' # in /private/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-50-04_register-wrapper_vlck6skr Registration parameters: type ........... im algo ........... syn slicewise ...... 1 metric ......... CC samplStrategy .. None samplPercent ... 0.2 iter ........... 1 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 (/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-53-10_register-slicewise_gcyalq2n) Copy input data to temp folder... Get image dimensions of destination image... matrix size: 448 x 448 x 20 voxel size: 0.5mm x 0.49999994mm x 20mm Split input volume... Split destination volume... Merge warping fields along z... Move warping fields... cp step3Warp.nii.gz /private/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-50-04_register-wrapper_vlck6skr cp step3InverseWarp.nii.gz /private/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-50-04_register-wrapper_vlck6skr rm -rf /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-53-10_register-slicewise_gcyalq2n Concatenate transformations... /Users/fmuhamma/sct_6.0/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_3.nii.gz warp_forward_2.nii.gz warp_forward_1.nii.gz /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w/warp_template2anat.nii.gz # in /private/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-50-04_register-wrapper_vlck6skr /Users/fmuhamma/sct_6.0/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w/warp_anat2template.nii.gz warp_inverse_1.nii.gz warp_inverse_2.nii.gz warp_inverse_3.nii.gz # in /private/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-50-04_register-wrapper_vlck6skr Apply transfo source --> dest... /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i src.nii -o src_reg.nii -t warp_src2dest.nii.gz -r dest.nii -n Linear # in /private/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-50-04_register-wrapper_vlck6skr Apply transfo dest --> source... /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i dest.nii -o dest_reg.nii -t warp_dest2src.nii.gz -r src.nii -n Linear # in /private/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-50-04_register-wrapper_vlck6skr Generate output files... File created: PAM50_t2s_reg.nii.gz mv /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-50-04_register-wrapper_vlck6skr/warp_src2dest.nii.gz warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz File created: warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz File created: sub-CSM070_ses-spinalcord_T2star_reg.nii.gz mv /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-50-04_register-wrapper_vlck6skr/warp_dest2src.nii.gz warp_sub-CSM070_ses-spinalcord_T2star2PAM50_t2s.nii.gz File created: warp_sub-CSM070_ses-spinalcord_T2star2PAM50_t2s.nii.gz Remove temporary files... rm -rf /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-50-04_register-wrapper_vlck6skr Finished! Elapsed time: 216s *** Generate Quality Control (QC) html report *** Resample images to 0.6x0.6 mm QcImage: layout with Axial slice Compute center of mass at each slice /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/ses-spinalcord/sub-CSM070/ses-spinalcord/T2star/sct_register_multimodal/2023_11_14_155341.882515/background_img.png Successfully generated the QC results in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/_json/qc_2023_11_14_155341.882515.json To see the results in a browser, type: open /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/index.html Done! To view results, run one of the following commands (depending on your preferred viewer): fsleyes /Users/FMUHAMMA/sct_6.0/data/PAM50/template/PAM50_t2s.nii.gz sub-CSM070_ses-spinalcord_T2star_reg.nii.gz & fslview_deprecated /Users/FMUHAMMA/sct_6.0/data/PAM50/template/PAM50_t2s.nii.gz sub-CSM070_ses-spinalcord_T2star_reg.nii.gz & fslview /Users/FMUHAMMA/sct_6.0/data/PAM50/template/PAM50_t2s.nii.gz sub-CSM070_ses-spinalcord_T2star_reg.nii.gz & Done! To view results, run one of the following commands (depending on your preferred viewer): fsleyes sub-CSM070_ses-spinalcord_T2star.nii.gz PAM50_t2s_reg.nii.gz & fslview_deprecated sub-CSM070_ses-spinalcord_T2star.nii.gz PAM50_t2s_reg.nii.gz & fslview sub-CSM070_ses-spinalcord_T2star.nii.gz PAM50_t2s_reg.nii.gz & + sct_warp_template -d sub-CSM070_ses-spinalcord_T2star.nii.gz -w warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -qc /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc -qc-subject sub-CSM070/ses-spinalcord -- Spinal Cord Toolbox (6.0) sct_warp_template -d sub-CSM070_ses-spinalcord_T2star.nii.gz -w warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -qc /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc -qc-subject sub-CSM070/ses-spinalcord -- Check parameters: Working directory ........ /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star Destination image ........ sub-CSM070_ses-spinalcord_T2star.nii.gz Warping field ............ warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz Path template ............ /Users/fmuhamma/sct_6.0/data/PAM50 Output folder ............ label WARP TEMPLATE: /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_t1.nii.gz -o label/template/PAM50_t1.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_t2.nii.gz -o label/template/PAM50_t2.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_t2s.nii.gz -o label/template/PAM50_t2s.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_cord.nii.gz -o label/template/PAM50_cord.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n NearestNeighbor # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_wm.nii.gz -o label/template/PAM50_wm.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_gm.nii.gz -o label/template/PAM50_gm.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_csf.nii.gz -o label/template/PAM50_csf.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n NearestNeighbor # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels.nii.gz -o label/template/PAM50_levels.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n NearestNeighbor # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_levels_continuous.nii.gz -o label/template/PAM50_levels_continuous.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_label_body.nii.gz -o label/template/PAM50_label_body.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_label_disc.nii.gz -o label/template/PAM50_label_disc.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_label_discPosterior.nii.gz -o label/template/PAM50_label_discPosterior.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_spine.nii.gz -o label/template/PAM50_spine.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_centerline.nii.gz -o label/template/PAM50_centerline.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/template/PAM50_label_spinal_levels.nii.gz -o label/template/PAM50_label_spinal_levels.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n NearestNeighbor # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star cp /Users/fmuhamma/sct_6.0/data/PAM50/template/info_label.txt label/template WARP ATLAS OF WHITE MATTER TRACTS: /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_00.nii.gz -o label/atlas/PAM50_atlas_00.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_01.nii.gz -o label/atlas/PAM50_atlas_01.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_02.nii.gz -o label/atlas/PAM50_atlas_02.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_03.nii.gz -o label/atlas/PAM50_atlas_03.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_04.nii.gz -o label/atlas/PAM50_atlas_04.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_05.nii.gz -o label/atlas/PAM50_atlas_05.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_06.nii.gz -o label/atlas/PAM50_atlas_06.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_07.nii.gz -o label/atlas/PAM50_atlas_07.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_08.nii.gz -o label/atlas/PAM50_atlas_08.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_09.nii.gz -o label/atlas/PAM50_atlas_09.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_10.nii.gz -o label/atlas/PAM50_atlas_10.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_11.nii.gz -o label/atlas/PAM50_atlas_11.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_12.nii.gz -o label/atlas/PAM50_atlas_12.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_13.nii.gz -o label/atlas/PAM50_atlas_13.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_14.nii.gz -o label/atlas/PAM50_atlas_14.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_15.nii.gz -o label/atlas/PAM50_atlas_15.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_16.nii.gz -o label/atlas/PAM50_atlas_16.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_17.nii.gz -o label/atlas/PAM50_atlas_17.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_18.nii.gz -o label/atlas/PAM50_atlas_18.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_19.nii.gz -o label/atlas/PAM50_atlas_19.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_20.nii.gz -o label/atlas/PAM50_atlas_20.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_21.nii.gz -o label/atlas/PAM50_atlas_21.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_22.nii.gz -o label/atlas/PAM50_atlas_22.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_23.nii.gz -o label/atlas/PAM50_atlas_23.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_24.nii.gz -o label/atlas/PAM50_atlas_24.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_25.nii.gz -o label/atlas/PAM50_atlas_25.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_26.nii.gz -o label/atlas/PAM50_atlas_26.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_27.nii.gz -o label/atlas/PAM50_atlas_27.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_28.nii.gz -o label/atlas/PAM50_atlas_28.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_29.nii.gz -o label/atlas/PAM50_atlas_29.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_30.nii.gz -o label/atlas/PAM50_atlas_30.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_31.nii.gz -o label/atlas/PAM50_atlas_31.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_32.nii.gz -o label/atlas/PAM50_atlas_32.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_33.nii.gz -o label/atlas/PAM50_atlas_33.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_34.nii.gz -o label/atlas/PAM50_atlas_34.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_35.nii.gz -o label/atlas/PAM50_atlas_35.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /Users/fmuhamma/sct_6.0/data/PAM50/atlas/PAM50_atlas_36.nii.gz -o label/atlas/PAM50_atlas_36.nii.gz -t warp_PAM50_t2s2sub-CSM070_ses-spinalcord_T2star.nii.gz -r sub-CSM070_ses-spinalcord_T2star.nii.gz -n Linear # in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2star cp /Users/fmuhamma/sct_6.0/data/PAM50/atlas/info_label.txt label/atlas *** Generate Quality Control (QC) html report *** Resample images to 0.6x0.6 mm QcImage: layout with Axial slice Compute center of mass at each slice /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/ses-spinalcord/sub-CSM070/ses-spinalcord/T2star/sct_warp_template/2023_11_14_155446.815471/background_img.png Successfully generated the QC results in /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/_json/qc_2023_11_14_155446.815471.json To see the results in a browser, type: open /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/index.html Done! To view results, run one of the following commands (depending on your preferred viewer): fsleyes sub-CSM070_ses-spinalcord_T2star.nii.gz -cm greyscale -a 100.0 label/template/PAM50_t2.nii.gz -cm greyscale -dr 0 4000 -a 100.0 label/template/PAM50_gm.nii.gz -cm red-yellow -dr 0.4 1 -a 50.0 label/template/PAM50_wm.nii.gz -cm blue-lightblue -dr 0.4 1 -a 50.0 & fslview_deprecated sub-CSM070_ses-spinalcord_T2star.nii.gz -l Greyscale -t 1 label/template/PAM50_t2.nii.gz -l Greyscale -b 0,4000 -t 1 label/template/PAM50_gm.nii.gz -l Red-Yellow -b 0.4,1 -t 0.5 label/template/PAM50_wm.nii.gz -l Blue-Lightblue -b 0.4,1 -t 0.5 & fslview sub-CSM070_ses-spinalcord_T2star.nii.gz -l Greyscale -t 1 label/template/PAM50_t2.nii.gz -l Greyscale -b 0,4000 -t 1 label/template/PAM50_gm.nii.gz -l Red-Yellow -b 0.4,1 -t 0.5 label/template/PAM50_wm.nii.gz -l Blue-Lightblue -b 0.4,1 -t 0.5 & + python /Users/FMUHAMMA/Desktop/Mri/utils/get_vertebral_coverage.py -vertfile ./label/template/PAM50_levels.nii.gz -subject sub-CSM070/ses-spinalcord -o /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/results/vert_coverage_t2star.csv /Users/FMUHAMMA/.pyenv/versions/Jupyter_notebook_3.9/bin/python: can't open file '/Users/FMUHAMMA/Desktop/Mri/utils/get_vertebral_coverage.py': [Errno 2] No such file or directory