+ 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/.DS_Store sent 924 bytes received 42 bytes 1.93K bytes/sec total size is 169.47M speedup is 175437.83 + 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/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/anat/sub-CSM070_ses-spinalcord_T2w_seg.nii.gz' Looking for manual segmentation: /Users/fmuhamma/Desktop/Mri/BIDS/derivatives/labels/sub-CSM070/ses-spinalcord/anat/sub-CSM070_ses-spinalcord_T2w_seg.nii.gz + [[ -e /Users/fmuhamma/Desktop/Mri/BIDS/derivatives/labels/sub-CSM070/ses-spinalcord/anat/sub-CSM070_ses-spinalcord_T2w_seg.nii.gz ]] + echo 'Found! Using manual segmentation.' Found! Using manual segmentation. + rsync -avzh /Users/fmuhamma/Desktop/Mri/BIDS/derivatives/labels/sub-CSM070/ses-spinalcord/anat/sub-CSM070_ses-spinalcord_T2w_seg.nii.gz sub-CSM070_ses-spinalcord_T2w_seg.nii.gz building file list ... done sub-CSM070_ses-spinalcord_T2w_seg.nii.gz sent 33.30K bytes received 42 bytes 66.69K bytes/sec total size is 33.13K speedup is 0.99 + sct_qc -i sub-CSM070_ses-spinalcord_T2w.nii.gz -s sub-CSM070_ses-spinalcord_T2w_seg.nii.gz -p sct_deepseg_sc -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_qc -i sub-CSM070_ses-spinalcord_T2w.nii.gz -s sub-CSM070_ses-spinalcord_T2w_seg.nii.gz -p sct_deepseg_sc -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 '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_153245.503080/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_153245.503080.json To see the results in a browser, type: open /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/qc/index.html + 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_15-32-47_label-vertebrae_lrdys34b) Copying input data to tmp folder... Straighten spinal cord... Creating temporary folder (/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-32-47_straighten-spinalcord_vpd7wlqw) Copy files to tmp folder... Fitting centerline using B-spline approximation Error on approximation = 3.48 mm Error on approximation = 1.0 mm Error on approximation = 1.08 mm Error on approximation = 0.61 mm Error on approximation = 0.43 mm Error on approximation = 0.35 mm Error on approximation = 0.34 mm Error on approximation = 0.34 mm Error on approximation = 0.34 mm Error on approximation = 0.34 mm Error on approximation = 0.32 mm Error on approximation = 0.29 mm Error on approximation = 0.27 mm Error on approximation = 0.23 mm Error on approximation = 0.22 mm Error on approximation = 0.22 mm Error on approximation = 0.22 mm Error on approximation = 0.23 mm Error on approximation = 0.22 mm Create the straight space and the safe zone Length of spinal cord: 221.4691314220215 Size of spinal cord in z direction: 203.34268160366364 Ratio length/size: 1.089142376186856 Safe zone boundaries (curved space): [-120.6348468159585, 82.70783478770514] Safe zone boundaries (straight space): [-129.69807172513742, 91.77105969688407] 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_15-32-47_straighten-spinalcord_vpd7wlqw Generate output files... mv /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-32-47_straighten-spinalcord_vpd7wlqw/tmp.curve2straight.nii.gz ./warp_curve2straight.nii.gz File created: ./warp_curve2straight.nii.gz mv /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-32-47_straighten-spinalcord_vpd7wlqw/tmp.straight2curve.nii.gz ./warp_straight2curve.nii.gz File created: ./warp_straight2curve.nii.gz cp /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-32-47_straighten-spinalcord_vpd7wlqw/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_15-32-47_straighten-spinalcord_vpd7wlqw 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_15-32-47_label-vertebrae_lrdys34b File /private/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-32-47_label-vertebrae_lrdys34b/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_15-33-20_detect-c2c3_mri_shb5) Run C2-C3 detector... C2-C3 detected... Remove temporary files... rm -rf /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-33-20_detect-c2c3_mri_shb5 File /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-32-47_label-vertebrae_lrdys34b/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_15-32-47_label-vertebrae_lrdys34b Get z and disc values from straight label... .. [350, 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=350). Direction: superior .. Peak found: z=-5 (correlation = 0.39807387992846166) Current disc: 1 (z=376). Direction: superior .. correcting factor: 1.0 .. Switching to inferior direction. Current disc: 3 (z=313). Direction: inferior .. Peak found: z=-5 (correlation = 0.4334537180118916) .. correcting factor: 1.0 Current disc: 4 (z=271). Direction: inferior .. Peak found: z=2 (correlation = 0.40193559711393856) .. correcting factor: 0.981981981981982 Current disc: 5 (z=241). Direction: inferior .. Peak found: z=-2 (correlation = 0.3269284660479923) .. correcting factor: 0.9940622440622441 Current disc: 6 (z=208). Direction: inferior .. Peak found: z=2 (correlation = 0.3953508626437765) .. correcting factor: 0.9823465694433435 Current disc: 7 (z=177). Direction: inferior .. Peak found: z=-1 (correlation = 0.38225995335985485) .. correcting factor: 0.9852888078694529 Current disc: 8 (z=134). Direction: inferior .. Peak found: z=6 (correlation = 0.3739332612421011) .. correcting factor: 0.964134592791757 Current disc: 9 (z=96). Direction: inferior .. Peak found: z=1 (correlation = 0.48844554812816643) .. correcting factor: 0.960465594779744 Current disc: 10 (z=53). Direction: inferior .. Peak found: z=5 (correlation = 0.48683515231958574) .. correcting factor: 0.9479500939104971 Current disc: 11 (z=12). Direction: inferior .. Peak found: z=5 (correlation = 0.48899709003863845) .. correcting factor: 0.9368285539072024 Adding top disc based on adjusted template distance: #0 .. approximate distance: 23 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_15-32-47_label-vertebrae_lrdys34b Cleaning labeled segmentation: removing labeled voxels outside segmentation... Done cleaning. File /private/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-32-47_label-vertebrae_lrdys34b/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_15-33-25_apply-transfo-3d-label_y3ac_jt3) /Users/fmuhamma/sct_6.0/bin/isct_antsApplyTransforms -d 3 -i /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-33-25_apply-transfo-3d-label_y3ac_jt3/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_15-32-47_label-vertebrae_lrdys34b Take the center of mass of each registered dilated labels... File segmentation_labeled_disc.nii already exists. Will overwrite it. Generate output files... File /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 already exists. Deleting it.. 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 /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 already exists. Deleting it.. 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 File /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w/straightening.cache already exists. Deleting it.. mv /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-32-47_label-vertebrae_lrdys34b/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 File /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w/warp_curve2straight.nii.gz already exists. Deleting it.. mv /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-32-47_label-vertebrae_lrdys34b/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 File /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w/warp_straight2curve.nii.gz already exists. Deleting it.. mv /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-32-47_label-vertebrae_lrdys34b/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 File /Users/fmuhamma/Desktop/Mri/sc_analysis_test_2023-09-1-all/data_processed/sub-CSM070/ses-spinalcord/anat/T2w/straight_ref.nii.gz already exists. Deleting it.. mv /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2023-11-14_15-32-47_label-vertebrae_lrdys34b/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_15-32-47_label-vertebrae_lrdys34b *** 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_153328.434369/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_153328.434369.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... File sub-CSM070_ses-spinalcord_T2w_seg_labeled_discs_1to9.nii.gz already exists. Will overwrite it. 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_15-33-43_register-to-template_lwzzsb5h) 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_15-33-45_straighten-spinalcord_yn0f8rlw) Copy files to tmp folder... Create the straight space and the safe zone Length of spinal cord: 48.595452486828194 Size of spinal cord in z direction: 47.92940469891818 Ratio length/size: 1.0138964335587721 Safe zone boundaries (curved space): [-12.59122845440848, 35.3381762445097] Safe zone boundaries (straight space): [-12.924252348363488, 35.671200138464705] 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'. Traceback (most recent call last): File "/Users/fmuhamma/sct_6.0/spinalcordtoolbox/scripts/sct_register_to_template.py", line 833, in main(sys.argv[1:]) File "/Users/fmuhamma/sct_6.0/spinalcordtoolbox/scripts/sct_register_to_template.py", line 565, in main sc_straight.straighten() File "/Users/fmuhamma/sct_6.0/spinalcordtoolbox/straightening.py", line 453, in straighten coord_straight2curved = centerline.get_inverse_plans_coordinates(coord_in_planes_straight, lookup) File "/Users/fmuhamma/sct_6.0/spinalcordtoolbox/types.py", line 330, in get_inverse_plans_coordinates return einsum('mnr,nr->mr', rollaxis(self.matrices[indexes], 0, 3), coordinates.transpose()).transpose() + self.points[indexes] IndexError: index 859 is out of bounds for axis 0 with size 49