Last login: Fri Feb 10 20:38:11 on ttys000 /Users/2391266776qq.com/.zprofile:1: no such file or directory: /opt/homebrew/bin/brew /Users/2391266776qq.com/.zprofile:4: no such file or directory: /usr/local/Homebrew/bin/brew 2391266776qq.com@ShydeMacBook-Pro ~ % la zsh: command not found: la 2391266776qq.com@ShydeMacBook-Pro ~ % ls Applications Pictures Desktop Public Documents Zotero Downloads iCloud云盘（归档） Library qc_CSM Movies qc_singleSubj Music sct_5.8 Parallels 2391266776qq.com@ShydeMacBook-Pro ~ % cd Downloads 2391266776qq.com@ShydeMacBook-Pro Downloads % ls 2023基金结题材料 22年中期考核暨23年硕博连读临床转博工作附件清单-给学生 A basic MRI anatomy of the rat brain in coronal sections for practical guidance to neuroscientists.pdf ADC.png BeeViewer CSM-SCT CSM复查患者 DWI.png FA.png MAGNITUDE.png MathWorks PHASE.png RSNA摘要 Siying T2 MAP.png T2WI.png software_package 资料 图片 1.png 附件1、关于填报《国家自然科学基金资助项目结题成果报告》的说明（2022版）.doc 附件2、项目资金决算编制说明.doc 附件3、经费决算说明书（例，仅供参考）.doc 附件4、2022年同济医院结题国家自然科学基金项目清单.xlsx 多模态 邵必读 - MR 动物实验 导师文章 临床伦理审查 医师注册文件 执业医师注册材料 首次执医注册操作流程及须知2022.12.23 2391266776qq.com@ShydeMacBook-Pro Downloads % cd CSM-SCT 2391266776qq.com@ShydeMacBook-Pro CSM-SCT % ls single_subject 2391266776qq.com@ShydeMacBook-Pro CSM-SCT % cd single_subject 2391266776qq.com@ShydeMacBook-Pro single_subject % ls data 2391266776qq.com@ShydeMacBook-Pro single_subject % cd data 2391266776qq.com@ShydeMacBook-Pro data % ls dmri t2 2391266776qq.com@ShydeMacBook-Pro data % cd t2 2391266776qq.com@ShydeMacBook-Pro t2 % ls t2 t2_OSag_T2FSE_20211031180636_10.nii.gz t2_OSag_T2FSE_20211031180636_10.json 2391266776qq.com@ShydeMacBook-Pro t2 % ls t2 t2.json t2.nii.gz 2391266776qq.com@ShydeMacBook-Pro t2 % sct_propseg -i t2.nii.gz -c t2 -qc ~/qc_singleSubj -- Spinal Cord Toolbox (5.8) sct_propseg -i t2.nii.gz -c t2 -qc /Users/2391266776qq.com/qc_singleSubj -- Creating temporary folder (/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230320214530.897163-propseg-oyff4pj7) Creating temporary folder (/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230320214530.933271-label_vertebrae-gf52w9ws) Creating temporary folder (/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230320214530.933770-vffq641l) Remove temporary files... rm -rf /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230320214530.933770-vffq641l /Users/2391266776qq.com/sct_5.8/bin/isct_propseg -t t2 -o /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230320214530.897163-propseg-oyff4pj7 -verbose -i /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2/t2.nii.gz -init-centerline /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230320214530.933271-label_vertebrae-gf52w9ws/centerline_optic.nii.gz -centerline-binary # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2 mv /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230320214530.897163-propseg-oyff4pj7/t2_seg.nii.gz ./t2_seg.nii.gz mv /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230320214530.897163-propseg-oyff4pj7/t2_centerline.nii.gz ./t2_centerline.nii.gz Check consistency of segmentation... Creating temporary folder (/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230320214542.653804-propseg-rf8d1pdj) /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230320214542.653804-propseg-rf8d1pdj/tmp.segmentation.nii.gz /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230320214542.653804-propseg-rf8d1pdj/tmp.centerline.nii.gz Get data dimensions... /Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/scripts/sct_propseg.py:83: DeprecationWarning: Please use `center_of_mass` from the `scipy.ndimage` namespace, the `scipy.ndimage.measurements` namespace is deprecated. x_centerline, y_centerline = ndi.measurements.center_of_mass(slice) /Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/scripts/sct_propseg.py:102: DeprecationWarning: Please use `center_of_mass` from the `scipy.ndimage` namespace, the `scipy.ndimage.measurements` namespace is deprecated. x_centerline, y_centerline = ndi.measurements.center_of_mass(slice) /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230320214542.653804-propseg-rf8d1pdj/tmp.segmentation_RPI_c.nii.gz rm -rf /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230320214542.653804-propseg-rf8d1pdj Copy header input --> output(s) to make sure qform is the same. Image header specifies datatype 'int16', but array is of type 'uint8'. Header metadata will be overwritten to use 'uint8'. File /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2/t2_seg.nii.gz already exists. Will overwrite it. Image header specifies datatype 'int16', but array is of type 'uint8'. Header metadata will be overwritten to use 'uint8'. File /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2/t2_centerline.nii.gz already exists. Will overwrite it. *** Generate Quality Control (QC) html report *** Resample images to 0.6x0.6 mm Image header specifies datatype 'int8', 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/2391266776qq.com/qc_singleSubj/single_subject/data/t2/sct_propseg/2023_03_20_214546.565788/bkg_img.png Successfully generated the QC results in /Users/2391266776qq.com/qc_singleSubj/_json/qc_2023_03_20_214546.565788.json To see the results in a browser, type: open /Users/2391266776qq.com/qc_singleSubj/index.html Done! To view results, run one of the following commands (depending on your preferred viewer): fslview_deprecated /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2/t2.nii.gz -l Greyscale /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2/t2_seg.nii.gz -l Red -t 1 & fslview /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2/t2.nii.gz -l Greyscale /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2/t2_seg.nii.gz -l Red -t 1 & 2391266776qq.com@ShydeMacBook-Pro t2 % sct_label_vertebrae -i t2.nii.gz -s t2_seg.nii.gz -c t2 -qc ~/qc_singleSubj -- Spinal Cord Toolbox (5.8) sct_label_vertebrae -i t2.nii.gz -s t2_seg.nii.gz -c t2 -qc /Users/2391266776qq.com/qc_singleSubj -- Creating temporary folder (/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230320234605.958674-label_vertebrae-mgtvwwhz) Copying input data to tmp folder... Straighten spinal cord... Creating temporary folder (/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230320234606.041628-straighten_spinalcord-x42n2i0c) Copy files to tmp folder... Fitting centerline using B-spline approximation Error on approximation = 6.43 mm Error on approximation = 5.34 mm Error on approximation = 4.0 mm Error on approximation = 2.76 mm Error on approximation = 2.92 mm Error on approximation = 1.38 mm Error on approximation = 1.11 mm Error on approximation = 1.03 mm Error on approximation = 1.02 mm Error on approximation = 0.96 mm Error on approximation = 0.96 mm Error on approximation = 0.94 mm Error on approximation = 0.95 mm Error on approximation = 0.86 mm Error on approximation = 0.95 mm Error on approximation = 0.78 mm Error on approximation = 0.61 mm Error on approximation = 0.59 mm Error on approximation = 0.57 mm Error on approximation = 0.46 mm Error on approximation = 0.34 mm Error on approximation = 0.34 mm Error on approximation = 0.45 mm Error on approximation = 0.47 mm Error on approximation = 0.36 mm Error on approximation = 0.23 mm Error on approximation = 0.21 mm Error on approximation = 0.26 mm Error on approximation = 0.24 mm Error on approximation = 0.18 mm Error on approximation = 0.2 mm Error on approximation = 0.16 mm Error on approximation = 0.17 mm Error on approximation = 0.16 mm Error on approximation = 0.14 mm Error on approximation = 0.13 mm Error on approximation = 0.15 mm Error on approximation = 0.12 mm Error on approximation = 0.12 mm Error on approximation = 0.12 mm Error on approximation = 0.11 mm Create the straight space and the safe zone Length of spinal cord: 263.9256162556736 Size of spinal cord in z direction: 257.1065341813771 Ratio length/size: 1.026522398958114 Safe zone boundaries (curved space): [-246.42547763059582, 10.681056550781278] Safe zone boundaries (straight space): [-249.83501866774407, 14.090597587929537] Pad input volume to account for spinal cord length... Time to generate centerline: 41.0 ms 100%|████████████████████████████████████████| 518/518 [00:01<00:00, 325.08it/s] 100%|█████████████████████████████████████████| 534/534 [00:08<00:00, 63.49it/s] Warping field generated: tmp.curve2straight.nii.gz Warping field generated: tmp.straight2curve.nii.gz Apply transformation to input image... /Users/2391266776qq.com/sct_5.8/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/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230320234606.041628-straighten_spinalcord-x42n2i0c Generate output files... mv /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230320234606.041628-straighten_spinalcord-x42n2i0c/tmp.curve2straight.nii.gz ./warp_curve2straight.nii.gz File created: ./warp_curve2straight.nii.gz mv /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230320234606.041628-straighten_spinalcord-x42n2i0c/tmp.straight2curve.nii.gz ./warp_straight2curve.nii.gz File created: ./warp_straight2curve.nii.gz cp /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230320234606.041628-straighten_spinalcord-x42n2i0c/tmp.anat_rigid_warp.nii.gz ./straight_ref.nii.gz File created: ./data_straight.nii Remove temporary files... rm -rf /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230320234606.041628-straighten_spinalcord-x42n2i0c Resample to 0.5mm isotropic... load data... Apply straightening to segmentation... /Users/2391266776qq.com/sct_5.8/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/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230320234605.958674-label_vertebrae-mgtvwwhz File /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230320234605.958674-label_vertebrae-mgtvwwhz/segmentation_straight.nii already exists. Will overwrite it. Create label to identify disc... Creating temporary folder... Creating temporary folder (/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230320234652.140916-sejurnet) Run C2-C3 detector... C2-C3 detected... Remove temporary files... rm -rf /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230320234652.140916-sejurnet File /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230320234605.958674-label_vertebrae-mgtvwwhz/labelz.nii.gz already exists. Will overwrite it. And apply straightening to label... /Users/2391266776qq.com/sct_5.8/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/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230320234605.958674-label_vertebrae-mgtvwwhz Get z and disc values from straight label... .. [291, 3] Look for template... Path template: /Users/2391266776qq.com/sct_5.8/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=291). Direction: superior .. Peak found: z=-8 (correlation = 0.4527060271933292) Current disc: 1 (z=314). Direction: superior .. correcting factor: 1.0 .. Switching to inferior direction. Current disc: 3 (z=254). Direction: inferior .. Peak found: z=-5 (correlation = 0.5859686730496729) .. correcting factor: 0.9594594594594594 Current disc: 4 (z=213). Direction: inferior .. Peak found: z=-9 (correlation = 0.4108990077590326) .. correcting factor: 1.045045045045045 Current disc: 5 (z=170). Direction: inferior .. Peak found: z=7 (correlation = 0.35930715025594256) .. correcting factor: 0.9883292383292384 Current disc: 6 (z=146). Direction: inferior .. Peak found: z=1 (correlation = 0.46300996701606) .. correcting factor: 0.9842117777601649 Current disc: 7 (z=114). Direction: inferior .. Peak found: z=3 (correlation = 0.40809442912813887) .. correcting factor: 0.9672353049962158 Current disc: 8 (z=75). Direction: inferior .. Peak found: z=2 (correlation = 0.4607773402329045) .. correcting factor: 0.9619491983024042 Current disc: 9 (z=33). Direction: inferior .. Peak found: z=-3 (correlation = 0.4532520520580313) .. correcting factor: 0.9694229398189516 Adding top disc based on adjusted template distance: #0 .. approximate distance: 24 Un-straighten labeling... /Users/2391266776qq.com/sct_5.8/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/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230320234605.958674-label_vertebrae-mgtvwwhz Cleaning labeled segmentation: removing labeled voxels outside segmentation... Done cleaning. File /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230320234605.958674-label_vertebrae-mgtvwwhz/segmentation_labeled.nii already exists. Will overwrite it. Label discs... Un-straighten labeled discs... Dilate labels before warping... Creating temporary folder (/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230320234654.779318-apply_transfo-1g8bp4dg) /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230320234654.779318-apply_transfo-1g8bp4dg/dilated_data.nii -o segmentation_labeled_disc.nii -t warp_straight2curve.nii.gz -r segmentation.nii -n NearestNeighbor # in /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230320234605.958674-label_vertebrae-mgtvwwhz 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/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2/t2_seg_labeled.nii.gz File created: /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2/t2_seg_labeled_discs.nii.gz mv /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230320234605.958674-label_vertebrae-mgtvwwhz/warp_curve2straight.nii.gz /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2/warp_curve2straight.nii.gz File created: /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2/warp_curve2straight.nii.gz mv /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230320234605.958674-label_vertebrae-mgtvwwhz/warp_straight2curve.nii.gz /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2/warp_straight2curve.nii.gz File created: /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2/warp_straight2curve.nii.gz mv /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230320234605.958674-label_vertebrae-mgtvwwhz/straight_ref.nii.gz /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2/straight_ref.nii.gz File created: /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2/straight_ref.nii.gz Remove temporary files... rm -rf /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230320234605.958674-label_vertebrae-mgtvwwhz *** Generate Quality Control (QC) html report *** Resample images to NonexNone mm QcImage: layout with Sagittal slice /Users/2391266776qq.com/qc_singleSubj/single_subject/data/t2/sct_label_vertebrae/2023_03_20_234656.594073/bkg_img.png Successfully generated the QC results in /Users/2391266776qq.com/qc_singleSubj/_json/qc_2023_03_20_234656.594073.json To see the results in a browser, type: open /Users/2391266776qq.com/qc_singleSubj/index.html Done! To view results, run one of the following commands (depending on your preferred viewer): fslview_deprecated /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2/t2.nii.gz -t 1 /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2/t2_seg_labeled.nii.gz -l MGH-Subcortical -t 0.5 & fslview /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2/t2.nii.gz -t 1 /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2/t2_seg_labeled.nii.gz -l MGH-Subcortical -t 0.5 & 2391266776qq.com@ShydeMacBook-Pro t2 % -vert-body zsh: command not found: -vert-body 2391266776qq.com@ShydeMacBook-Pro t2 % ls straight_ref.nii.gz t2_seg.nii.gz straightening.cache t2_seg_labeled.nii.gz t2 t2_seg_labeled_discs.nii.gz t2.json warp_curve2straight.nii.gz t2.nii.gz warp_straight2curve.nii.gz t2_centerline.nii.gz 2391266776qq.com@ShydeMacBook-Pro t2 % sct_label_utils -i t2_seg_labeled_discs.nii.gz -vert-body 3,4,5,6,7 -o t2_labels_disc.nii.gz -- Spinal Cord Toolbox (5.8) sct_label_utils -i t2_seg_labeled_discs.nii.gz -vert-body 3,4,5,6,7 -o t2_labels_disc.nii.gz -- Generating output files... Done! To view results, run one of the following commands (depending on your preferred viewer): fslview_deprecated t2_seg_labeled_discs.nii.gz t2_labels_disc.nii.gz & fslview t2_seg_labeled_discs.nii.gz t2_labels_disc.nii.gz & 2391266776qq.com@ShydeMacBook-Pro t2 % sct_register_to_template -i t2.nii.gz -s t2_seg.nii.gz -l t2_labels_discs.nii.gz -c t2 -qc ~/qc_singleSubj -- Spinal Cord Toolbox (5.8) sct_register_to_template -i t2.nii.gz -s t2_seg.nii.gz -l t2_labels_discs.nii.gz -c t2 -qc /Users/2391266776qq.com/qc_singleSubj -- Check template files... OK: /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_t2.nii.gz OK: /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_levels.nii.gz OK: /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_cord.nii.gz Check parameters: Data: t2.nii.gz Landmarks: t2_labels_discs.nii.gz Segmentation: t2_seg.nii.gz Path template: /Users/2391266776qq.com/sct_5.8/data/PAM50 Remove temp files: 1 Check input labels... Traceback (most recent call last): File "/Users/2391266776qq.com/sct_5.8/python/envs/venv_sct/lib/python3.8/site-packages/nibabel/loadsave.py", line 42, in load stat_result = os.stat(filename) FileNotFoundError: [Errno 2] No such file or directory: '/Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2/t2_labels_discs.nii.gz' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/scripts/sct_register_to_template.py", line 817, in main(sys.argv[1:]) File "/Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/scripts/sct_register_to_template.py", line 398, in main labels = check_labels(fname_landmarks, label_type=label_type) File "/Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/registration/labeling.py", line 143, in check_labels image_label = Image(fname_landmarks) File "/Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/image.py", line 289, in __init__ raise e File "/Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/image.py", line 284, in __init__ self.loadFromPath(param, mmap, verbose) File "/Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/image.py", line 432, in loadFromPath im_file = nib.load(self.absolutepath, mmap=mmap) File "/Users/2391266776qq.com/sct_5.8/python/envs/venv_sct/lib/python3.8/site-packages/nibabel/loadsave.py", line 44, in load raise FileNotFoundError(f"No such file or no access: '{filename}'") FileNotFoundError: No such file or no access: '/Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2/t2_labels_discs.nii.gz' 2391266776qq.com@ShydeMacBook-Pro t2 % sct_register_to_template -i t2.nii.gz -s t2_seg.nii.gz -ldisc t2_labels_discs.nii.gz -c t2 -qc ~/qc_singleSubj -- Spinal Cord Toolbox (5.8) sct_register_to_template -i t2.nii.gz -s t2_seg.nii.gz -ldisc t2_labels_discs.nii.gz -c t2 -qc /Users/2391266776qq.com/qc_singleSubj -- Check template files... OK: /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_t2.nii.gz OK: /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_label_disc.nii.gz OK: /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_cord.nii.gz Check parameters: Data: t2.nii.gz Landmarks: t2_labels_discs.nii.gz Segmentation: t2_seg.nii.gz Path template: /Users/2391266776qq.com/sct_5.8/data/PAM50 Remove temp files: 1 Check input labels... Traceback (most recent call last): File "/Users/2391266776qq.com/sct_5.8/python/envs/venv_sct/lib/python3.8/site-packages/nibabel/loadsave.py", line 42, in load stat_result = os.stat(filename) FileNotFoundError: [Errno 2] No such file or directory: '/Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2/t2_labels_discs.nii.gz' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/scripts/sct_register_to_template.py", line 817, in main(sys.argv[1:]) File "/Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/scripts/sct_register_to_template.py", line 398, in main labels = check_labels(fname_landmarks, label_type=label_type) File "/Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/registration/labeling.py", line 143, in check_labels image_label = Image(fname_landmarks) File "/Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/image.py", line 289, in __init__ raise e File "/Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/image.py", line 284, in __init__ self.loadFromPath(param, mmap, verbose) File "/Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/image.py", line 432, in loadFromPath im_file = nib.load(self.absolutepath, mmap=mmap) File "/Users/2391266776qq.com/sct_5.8/python/envs/venv_sct/lib/python3.8/site-packages/nibabel/loadsave.py", line 44, in load raise FileNotFoundError(f"No such file or no access: '{filename}'") FileNotFoundError: No such file or no access: '/Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2/t2_labels_discs.nii.gz' 2391266776qq.com@ShydeMacBook-Pro t2 % sct_register_to_template -i t2.nii.gz -s t2_seg.nii.gz -l t2_labels_disc.nii.gz -c t2 -qc ~/qc_singleSubj -- Spinal Cord Toolbox (5.8) sct_register_to_template -i t2.nii.gz -s t2_seg.nii.gz -l t2_labels_disc.nii.gz -c t2 -qc /Users/2391266776qq.com/qc_singleSubj -- Check template files... OK: /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_t2.nii.gz OK: /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_levels.nii.gz OK: /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_cord.nii.gz Check parameters: Data: t2.nii.gz Landmarks: t2_labels_disc.nii.gz Segmentation: t2_seg.nii.gz Path template: /Users/2391266776qq.com/sct_5.8/data/PAM50 Remove temp files: 1 Check input labels... Creating temporary folder (/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001440.598945-register_to_template-2l5rmsxm) Copying input data to tmp folder and convert to nii... Generate labels from template vertebral labeling Check if provided labels are available in the template Binarize segmentation Image header specifies datatype 'int8', but array is of type ''. Header metadata will be overwritten to use ''. Resample data to 1mm isotropic... load data... Done! To view results, run one of the following commands (depending on your preferred viewer): 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): 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/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001443.943489-straighten_spinalcord-98emqgsp) Copy files to tmp folder... Create the straight space and the safe zone Length of spinal cord: 263.64432997173935 Size of spinal cord in z direction: 256.665653746678 Ratio length/size: 1.0271897549328868 Safe zone boundaries (curved space): [-246.46637695849503, 10.19927678818297] Safe zone boundaries (straight space): [-249.9557150710257, 13.688614900713645] Pad input volume to account for spinal cord length... Time to generate centerline: 19.0 ms 100%|█████████████████████████████████████████| 263/263 [00:03<00:00, 73.21it/s] 100%|█████████████████████████████████████████| 272/272 [00:07<00:00, 37.90it/s] Warping field generated: tmp.curve2straight.nii.gz Warping field generated: tmp.straight2curve.nii.gz Apply transformation to input image... /Users/2391266776qq.com/sct_5.8/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/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001443.943489-straighten_spinalcord-98emqgsp Generate output files... mv /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001443.943489-straighten_spinalcord-98emqgsp/tmp.curve2straight.nii.gz ./warp_curve2straight.nii.gz File created: ./warp_curve2straight.nii.gz mv /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001443.943489-straighten_spinalcord-98emqgsp/tmp.straight2curve.nii.gz ./warp_straight2curve.nii.gz File created: ./warp_straight2curve.nii.gz cp /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001443.943489-straighten_spinalcord-98emqgsp/tmp.anat_rigid_warp.nii.gz ./straight_ref.nii.gz mv /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001443.943489-straighten_spinalcord-98emqgsp/tmp.anat_rigid_warp.nii.gz /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001440.598945-register_to_template-2l5rmsxm/seg_bin_1mm_rpi_crop_straight.nii.gz File created: /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001440.598945-register_to_template-2l5rmsxm/seg_bin_1mm_rpi_crop_straight.nii.gz Remove temporary files... rm -rf /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001443.943489-straighten_spinalcord-98emqgsp /Users/2391266776qq.com/sct_5.8/bin/isct_ComposeMultiTransform 3 warp_straight2curve.nii.gz -R /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001440.598945-register_to_template-2l5rmsxm/data_1mm_rpi.nii warp_straight2curve.nii.gz # in /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001440.598945-register_to_template-2l5rmsxm Remove unused label on template. Keep only label present in the input label image... File template_label_body.nii.gz already exists. Will overwrite it. Dilating input labels using 3vox ball radius Apply straightening to labels... /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001440.598945-register_to_template-2l5rmsxm/label_projected_1mm_rpi_dilate.nii.gz -o /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001440.598945-register_to_template-2l5rmsxm/label_projected_1mm_rpi_dilate_straight.nii.gz -t warp_curve2straight.nii.gz -r /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001440.598945-register_to_template-2l5rmsxm/seg_bin_1mm_rpi_crop_straight.nii.gz -n NearestNeighbor # in /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001440.598945-register_to_template-2l5rmsxm Estimate transformation for step #0... Labels src: [[-1.5659025553613901, 30.622025582473725, -112.59143809974194], [-1.3703321256442003, 32.81794424353211, -130.5063024656614], [-1.1859103813694674, 34.930481948831584, -152.3962603493128], [-1.0526280244400272, 36.92521061217083, -166.37005963934735], [-0.9212036896497011, 38.42692584125325, -180.1372743099928]] Labels dest: [[-0.0, 45.720001220703125, -117.34002685546875], [-0.0, 45.720001220703125, -135.84002685546875], [-0.0, 45.720001220703125, -153.34002685546875], [-0.0, 45.720001220703125, -169.34002685546875], [-0.0, 45.720001220703125, -185.34002685546875]] Degrees of freedom (dof): Tx_Ty_Tz_Sz Optimization terminated successfully. Current function value: 53.080727 Iterations: 2 Function evaluations: 166 Matrix: [[ 1. 0. 0.] [ 0. 1. 0.] [-0. 0. 1.]] Center: [ 0. 45.72000122 -152.24002686] Translation: [[ -1.21919536 -10.97548358 3.83975988]] Concatenate transformations: curve --> straight --> affine... /Users/2391266776qq.com/sct_5.8/bin/isct_ComposeMultiTransform 3 warp_curve2straightAffine.nii.gz -R template.nii straight2templateAffine.txt warp_curve2straight.nii.gz # in /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001440.598945-register_to_template-2l5rmsxm Apply transformation... /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001440.598945-register_to_template-2l5rmsxm/data_1mm_rpi.nii -o /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001440.598945-register_to_template-2l5rmsxm/data_1mm_rpi_straightAffine.nii -t warp_curve2straightAffine.nii.gz -r template.nii -n 'BSpline[3]' # in /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001440.598945-register_to_template-2l5rmsxm /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001440.598945-register_to_template-2l5rmsxm/seg_bin_1mm_rpi_crop.nii.gz -o /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001440.598945-register_to_template-2l5rmsxm/seg_bin_1mm_rpi_crop_straightAffine.nii.gz -t warp_curve2straightAffine.nii.gz -r template.nii -n Linear # in /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001440.598945-register_to_template-2l5rmsxm 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/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001514.430761-register-mf7vehuw) 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/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001514.636813-register-vp_3d7ck) Copy input data to temp folder... Get image dimensions of destination image... matrix size: 141 x 141 x 95 voxel size: 0.5mm x 0.5mm x 95mm Split input segmentation... Split destination segmentation... Split input image... Split destination image... Estimate cord angle for each slice: 0%| | 0/95 [00:00 step1Warp.nii.gz Generate warping field... --> step1InverseWarp.nii.gz Move warping fields... cp step1Warp.nii.gz /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001514.430761-register-mf7vehuw cp step1InverseWarp.nii.gz /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001514.430761-register-mf7vehuw rm -rf /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001514.636813-register-vp_3d7ck -- ESTIMATE TRANSFORMATION FOR STEP #2 Apply transformation from previous step /Users/2391266776qq.com/sct_5.8/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/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001514.430761-register-mf7vehuw 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/2391266776qq.com/sct_5.8/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/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001514.430761-register-mf7vehuw Concatenate transformations... /Users/2391266776qq.com/sct_5.8/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/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001514.430761-register-mf7vehuw /Users/2391266776qq.com/sct_5.8/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/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001514.430761-register-mf7vehuw Apply transfo source --> dest... /Users/2391266776qq.com/sct_5.8/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/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001514.430761-register-mf7vehuw Apply transfo dest --> source... /Users/2391266776qq.com/sct_5.8/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/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001514.430761-register-mf7vehuw Generate output files... mv /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001514.430761-register-mf7vehuw/src_reg.nii data_1mm_rpi_straightAffine_crop_sub_reg.nii File created: data_1mm_rpi_straightAffine_crop_sub_reg.nii mv /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001514.430761-register-mf7vehuw/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/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001514.430761-register-mf7vehuw/dest_reg.nii template_crop_sub_reg.nii File created: template_crop_sub_reg.nii mv /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001514.430761-register-mf7vehuw/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/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001514.430761-register-mf7vehuw Concatenate transformations: anat --> template... /Users/2391266776qq.com/sct_5.8/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/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001440.598945-register_to_template-2l5rmsxm Concatenate transformations: template --> anat... /Users/2391266776qq.com/sct_5.8/bin/isct_ComposeMultiTransform 3 warp_template2anat.nii.gz -R data.nii warp_straight2curve.nii.gz -i straight2templateAffine.txt warp_template_crop_sub2data_1mm_rpi_straightAffine_crop_sub.nii.gz # in /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001440.598945-register_to_template-2l5rmsxm /Users/2391266776qq.com/sct_5.8/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/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001440.598945-register_to_template-2l5rmsxm /Users/2391266776qq.com/sct_5.8/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/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001440.598945-register_to_template-2l5rmsxm Generate output files... mv /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001440.598945-register_to_template-2l5rmsxm/warp_template2anat.nii.gz warp_template2anat.nii.gz File created: warp_template2anat.nii.gz mv /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001440.598945-register_to_template-2l5rmsxm/warp_anat2template.nii.gz warp_anat2template.nii.gz File created: warp_anat2template.nii.gz mv /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001440.598945-register_to_template-2l5rmsxm/template2anat.nii.gz template2anat.nii.gz File created: template2anat.nii.gz mv /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001440.598945-register_to_template-2l5rmsxm/anat2template.nii.gz anat2template.nii.gz File created: anat2template.nii.gz File warp_curve2straight.nii.gz already exists. Deleting it.. mv /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001440.598945-register_to_template-2l5rmsxm/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/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001440.598945-register_to_template-2l5rmsxm/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/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001440.598945-register_to_template-2l5rmsxm/straight_ref.nii.gz straight_ref.nii.gz File created: straight_ref.nii.gz Delete temporary files... rm -rf /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001440.598945-register_to_template-2l5rmsxm Finished! Elapsed time: 95s *** Generate Quality Control (QC) html report *** Resample images to 0.6x0.6 mm Image header specifies datatype 'int8', 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/2391266776qq.com/qc_singleSubj/single_subject/data/t2/sct_register_to_template/2023_03_21_001622.399538/bkg_img.png Successfully generated the QC results in /Users/2391266776qq.com/qc_singleSubj/_json/qc_2023_03_21_001622.399538.json To see the results in a browser, type: open /Users/2391266776qq.com/qc_singleSubj/index.html Done! To view results, run one of the following commands (depending on your preferred viewer): fslview_deprecated t2.nii.gz template2anat.nii.gz & fslview t2.nii.gz template2anat.nii.gz & Done! To view results, run one of the following commands (depending on your preferred viewer): fslview_deprecated /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_t2.nii.gz anat2template.nii.gz & fslview /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_t2.nii.gz anat2template.nii.gz & 2391266776qq.com@ShydeMacBook-Pro t2 % sct_register_to_template -i t2.nii.gz -s t2_seg.nii.gz -ldisc t2_labels_disc.nii.gz -c t2 -qc ~/qc_singleSubj -- Spinal Cord Toolbox (5.8) sct_register_to_template -i t2.nii.gz -s t2_seg.nii.gz -ldisc t2_labels_disc.nii.gz -c t2 -qc /Users/2391266776qq.com/qc_singleSubj -- Check template files... OK: /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_t2.nii.gz OK: /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_label_disc.nii.gz OK: /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_cord.nii.gz Check parameters: Data: t2.nii.gz Landmarks: t2_labels_disc.nii.gz Segmentation: t2_seg.nii.gz Path template: /Users/2391266776qq.com/sct_5.8/data/PAM50 Remove temp files: 1 Check input labels... Creating temporary folder (/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001838.861232-register_to_template-zwvf9lr2) Copying input data to tmp folder and convert to nii... Check if provided labels are available in the template Binarize segmentation Image header specifies datatype 'int8', but array is of type ''. Header metadata will be overwritten to use ''. Resample data to 1mm isotropic... load data... Done! To view results, run one of the following commands (depending on your preferred viewer): 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): 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/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001841.022857-straighten_spinalcord-3q1j_gla) Copy files to tmp folder... Create the straight space and the safe zone Length of spinal cord: 87.59235545142155 Size of spinal cord in z direction: 85.65692386262069 Ratio length/size: 1.0225951563694369 Safe zone boundaries (curved space): [-184.60644875799986, -98.94952489537917] Safe zone boundaries (straight space): [-185.5741645524003, -97.98180910097874] 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'. 100%|█████████████████████████████████████████| 991/991 [00:58<00:00, 17.00it/s] 100%|███████████████████████████████████████████| 88/88 [00:02<00:00, 40.66it/s] 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/2391266776qq.com/sct_5.8/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/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001841.022857-straighten_spinalcord-3q1j_gla Generate output files... mv /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001841.022857-straighten_spinalcord-3q1j_gla/tmp.curve2straight.nii.gz ./warp_curve2straight.nii.gz File created: ./warp_curve2straight.nii.gz mv /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001841.022857-straighten_spinalcord-3q1j_gla/tmp.straight2curve.nii.gz ./warp_straight2curve.nii.gz File created: ./warp_straight2curve.nii.gz cp /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001841.022857-straighten_spinalcord-3q1j_gla/tmp.anat_rigid_warp.nii.gz ./straight_ref.nii.gz mv /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001841.022857-straighten_spinalcord-3q1j_gla/tmp.anat_rigid_warp.nii.gz /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001838.861232-register_to_template-zwvf9lr2/seg_bin_1mm_rpi_crop_straight.nii.gz File created: /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001838.861232-register_to_template-zwvf9lr2/seg_bin_1mm_rpi_crop_straight.nii.gz Remove temporary files... rm -rf /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001841.022857-straighten_spinalcord-3q1j_gla /Users/2391266776qq.com/sct_5.8/bin/isct_ComposeMultiTransform 3 warp_straight2curve.nii.gz -R /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001838.861232-register_to_template-zwvf9lr2/data_1mm_rpi.nii warp_straight2curve.nii.gz # in /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001838.861232-register_to_template-zwvf9lr2 cp warp_curve2straight.nii.gz warp_curve2straightAffine.nii.gz Apply transformation... /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001838.861232-register_to_template-zwvf9lr2/data_1mm_rpi.nii -o /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001838.861232-register_to_template-zwvf9lr2/data_1mm_rpi_straightAffine.nii -t warp_curve2straightAffine.nii.gz -r template.nii -n 'BSpline[3]' # in /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001838.861232-register_to_template-zwvf9lr2 /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001838.861232-register_to_template-zwvf9lr2/seg_bin_1mm_rpi_crop.nii.gz -o /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001838.861232-register_to_template-zwvf9lr2/seg_bin_1mm_rpi_crop_straightAffine.nii.gz -t warp_curve2straightAffine.nii.gz -r template.nii -n Linear # in /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001838.861232-register_to_template-zwvf9lr2 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/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001957.192154-register-fpgpal03) 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/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001957.324524-register-yv72xd8m) Copy input data to temp folder... Get image dimensions of destination image... matrix size: 141 x 141 x 44 voxel size: 0.5mm x 0.5mm x 44mm Split input segmentation... Split destination segmentation... Split input image... Split destination image... Estimate cord angle for each slice: 0%| | 0/44 [00:00 step1Warp.nii.gz Generate warping field... --> step1InverseWarp.nii.gz Move warping fields... cp step1Warp.nii.gz /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001957.192154-register-fpgpal03 cp step1InverseWarp.nii.gz /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001957.192154-register-fpgpal03 rm -rf /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001957.324524-register-yv72xd8m -- ESTIMATE TRANSFORMATION FOR STEP #2 Apply transformation from previous step /Users/2391266776qq.com/sct_5.8/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/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001957.192154-register-fpgpal03 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/2391266776qq.com/sct_5.8/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/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001957.192154-register-fpgpal03 Concatenate transformations... /Users/2391266776qq.com/sct_5.8/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/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001957.192154-register-fpgpal03 /Users/2391266776qq.com/sct_5.8/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/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001957.192154-register-fpgpal03 Apply transfo source --> dest... /Users/2391266776qq.com/sct_5.8/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/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001957.192154-register-fpgpal03 Apply transfo dest --> source... /Users/2391266776qq.com/sct_5.8/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/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001957.192154-register-fpgpal03 Generate output files... mv /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001957.192154-register-fpgpal03/src_reg.nii data_1mm_rpi_straightAffine_crop_sub_reg.nii File created: data_1mm_rpi_straightAffine_crop_sub_reg.nii mv /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001957.192154-register-fpgpal03/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/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001957.192154-register-fpgpal03/dest_reg.nii template_crop_sub_reg.nii File created: template_crop_sub_reg.nii mv /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001957.192154-register-fpgpal03/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/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001957.192154-register-fpgpal03 Concatenate transformations: anat --> template... /Users/2391266776qq.com/sct_5.8/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/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001838.861232-register_to_template-zwvf9lr2 Concatenate transformations: template --> anat... /Users/2391266776qq.com/sct_5.8/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/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001838.861232-register_to_template-zwvf9lr2 /Users/2391266776qq.com/sct_5.8/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/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001838.861232-register_to_template-zwvf9lr2 /Users/2391266776qq.com/sct_5.8/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/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001838.861232-register_to_template-zwvf9lr2 Generate output files... mv /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001838.861232-register_to_template-zwvf9lr2/warp_template2anat.nii.gz warp_template2anat.nii.gz File created: warp_template2anat.nii.gz mv /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001838.861232-register_to_template-zwvf9lr2/warp_anat2template.nii.gz warp_anat2template.nii.gz File created: warp_anat2template.nii.gz mv /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001838.861232-register_to_template-zwvf9lr2/template2anat.nii.gz template2anat.nii.gz File created: template2anat.nii.gz mv /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001838.861232-register_to_template-zwvf9lr2/anat2template.nii.gz anat2template.nii.gz File created: anat2template.nii.gz File warp_curve2straight.nii.gz already exists. Deleting it.. mv /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001838.861232-register_to_template-zwvf9lr2/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/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001838.861232-register_to_template-zwvf9lr2/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/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001838.861232-register_to_template-zwvf9lr2/straight_ref.nii.gz straight_ref.nii.gz File created: straight_ref.nii.gz Delete temporary files... rm -rf /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321001838.861232-register_to_template-zwvf9lr2 Finished! Elapsed time: 115s *** Generate Quality Control (QC) html report *** Resample images to 0.6x0.6 mm Image header specifies datatype 'int8', 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/2391266776qq.com/qc_singleSubj/single_subject/data/t2/sct_register_to_template/2023_03_21_002040.019112/bkg_img.png Successfully generated the QC results in /Users/2391266776qq.com/qc_singleSubj/_json/qc_2023_03_21_002040.019112.json To see the results in a browser, type: open /Users/2391266776qq.com/qc_singleSubj/index.html Done! To view results, run one of the following commands (depending on your preferred viewer): fslview_deprecated t2.nii.gz template2anat.nii.gz & fslview t2.nii.gz template2anat.nii.gz & Done! To view results, run one of the following commands (depending on your preferred viewer): fslview_deprecated /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_t2.nii.gz anat2template.nii.gz & fslview /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_t2.nii.gz anat2template.nii.gz & 2391266776qq.com@ShydeMacBook-Pro t2 % sct_warp_template -d t2.nii.gz -w warp_template2anat.nii.gz -a 0 -qc ~/qc_singleSubj -- Spinal Cord Toolbox (5.8) sct_warp_template -d t2.nii.gz -w warp_template2anat.nii.gz -a 0 -qc /Users/2391266776qq.com/qc_singleSubj -- Check parameters: Working directory ........ /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2 Destination image ........ t2.nii.gz Warping field ............ warp_template2anat.nii.gz Path template ............ /Users/2391266776qq.com/sct_5.8/data/PAM50 Output folder ............ label WARP TEMPLATE: /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_t1.nii.gz -o label/template/PAM50_t1.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2 /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_t2.nii.gz -o label/template/PAM50_t2.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2 /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_t2s.nii.gz -o label/template/PAM50_t2s.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2 /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_cord.nii.gz -o label/template/PAM50_cord.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n NearestNeighbor # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2 /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_wm.nii.gz -o label/template/PAM50_wm.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2 /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_gm.nii.gz -o label/template/PAM50_gm.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2 /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_csf.nii.gz -o label/template/PAM50_csf.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n NearestNeighbor # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2 /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_levels.nii.gz -o label/template/PAM50_levels.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n NearestNeighbor # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2 /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_levels_continuous.nii.gz -o label/template/PAM50_levels_continuous.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2 /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_label_body.nii.gz -o label/template/PAM50_label_body.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2 /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_label_disc.nii.gz -o label/template/PAM50_label_disc.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2 /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_label_discPosterior.nii.gz -o label/template/PAM50_label_discPosterior.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2 /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_spine.nii.gz -o label/template/PAM50_spine.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2 /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_centerline.nii.gz -o label/template/PAM50_centerline.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2 /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_label_spinal_levels.nii.gz -o label/template/PAM50_label_spinal_levels.nii.gz -t warp_template2anat.nii.gz -r t2.nii.gz -n NearestNeighbor # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2 cp /Users/2391266776qq.com/sct_5.8/data/PAM50/template/info_label.txt label/template *** 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/2391266776qq.com/sct_5.8/python/envs/venv_sct/lib/python3.8/site-packages/scipy/ndimage/_measurements.py:1407: RuntimeWarning: invalid value encountered in double_scalars results = [sum(input * grids[dir].astype(float), labels, index) / normalizer /Users/2391266776qq.com/qc_singleSubj/single_subject/data/t2/sct_warp_template/2023_03_21_002157.879671/bkg_img.png Successfully generated the QC results in /Users/2391266776qq.com/qc_singleSubj/_json/qc_2023_03_21_002157.879671.json To see the results in a browser, type: open /Users/2391266776qq.com/qc_singleSubj/index.html Done! To view results, run one of the following commands (depending on your preferred viewer): fslview_deprecated t2.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 t2.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 & 2391266776qq.com@ShydeMacBook-Pro t2 % cd .. 2391266776qq.com@ShydeMacBook-Pro data % ls dmri t2 2391266776qq.com@ShydeMacBook-Pro data % cd dmri 2391266776qq.com@ShydeMacBook-Pro dmri % ls dmri dmri.bval dmri.bvec dmri.json dmri.nii.gz 2391266776qq.com@ShydeMacBook-Pro dmri % sct_dmri_separate_b0_and_dwi -i dmri.nii.gz -bvec dmri.bvec.txt -- Spinal Cord Toolbox (5.8) sct_dmri_separate_b0_and_dwi -i dmri.nii.gz -bvec dmri.bvec.txt -- Input parameters: input file ............dmri.nii.gz bvecs file ............dmri.bvec.txt bvals file ............ average ...............1 Creating temporary folder (/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321002902.643564-dmri_separate-jw4y2iaf) Copy files into temporary folder... Traceback (most recent call last): File "/Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/scripts/sct_dmri_separate_b0_and_dwi.py", line 320, in main(sys.argv[1:]) File "/Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/scripts/sct_dmri_separate_b0_and_dwi.py", line 164, in main copy(fname_bvecs, os.path.join(path_tmp, "bvecs"), verbose=verbose) File "/Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/utils/fs.py", line 239, in copy raise Exception("Couldn't find %s in %s (contents: %s)" Exception: Couldn't find dmri.bvec.txt in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri (contents: ['.DS_Store', 'dmri.json', 'dmri.bval', 'dmri.nii.gz', 'dmri', 'dmri.bvec']) 2391266776qq.com@ShydeMacBook-Pro dmri % sct_dmri_separate_b0_and_dwi -i dmri.nii.gz -bvec dmri.bvec -- Spinal Cord Toolbox (5.8) sct_dmri_separate_b0_and_dwi -i dmri.nii.gz -bvec dmri.bvec -- Input parameters: input file ............dmri.nii.gz bvecs file ............dmri.bvec bvals file ............ average ...............1 Creating temporary folder (/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321002940.361698-dmri_separate-_204s_oo) Copy files into temporary folder... cp /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri/dmri.bvec /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321002940.361698-dmri_separate-_204s_oo/bvecs Get dimensions data... .. 256 x 256 x 25 x 13 Identify b=0 and DWI images... WARNING: bvecs file is 3xn instead of nx3. Consider using sct_dmri_transpose_bvecs. Transpose bvecs... Number of b=0: 1 [0] Number of DWI: 12 [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12] Split along T dimension... Merge b=0... Average b=0... Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'. Average DWI... Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'. Generate output files... File created: /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri/dmri_b0.nii.gz File created: /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri/dmri_dwi.nii.gz File created: /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri/dmri_b0_mean.nii.gz File created: /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri/dmri_dwi_mean.nii.gz Remove temporary files... rm -rf /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321002940.361698-dmri_separate-_204s_oo Finished! Elapsed time: 2s 2391266776qq.com@ShydeMacBook-Pro dmri % sct_deepseg_sc -i dmri_dwi_mean.nii.gz -c dwi -qc ~/qc_singleSubj -- Spinal Cord Toolbox (5.8) sct_deepseg_sc -i dmri_dwi_mean.nii.gz -c dwi -qc /Users/2391266776qq.com/qc_singleSubj -- Config deepseg_sc: Centerline algorithm: svm Brain in image: False Kernel dimension: 2d Contrast: dwi Threshold: 0.01 Creating temporary folder (/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321003016.794674-2czvhxzi) Reorient the image to RPI, if necessary... Finding the spinal cord centerline... Creating temporary folder (/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321003017.648245-hy9tsnmf) Remove temporary files... rm -rf /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321003017.648245-hy9tsnmf Cropping the image around the spinal cord... Normalizing the intensity... Segmenting the spinal cord using deep learning on 2D patches... Reassembling the image... Resampling the segmentation to the native image resolution using linear interpolation... Binarizing the resampled segmentation... Image header specifies datatype 'float32', but array is of type 'uint8'. Header metadata will be overwritten to use 'uint8'. Compute shape analysis: 100%|################| 25/25 [00:00<00:00, 252.86iter/s] Remove temporary files... rm -rf /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321003016.794674-2czvhxzi *** 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/2391266776qq.com/qc_singleSubj/single_subject/data/dmri/sct_deepseg_sc/2023_03_21_003020.263011/bkg_img.png Successfully generated the QC results in /Users/2391266776qq.com/qc_singleSubj/_json/qc_2023_03_21_003020.263011.json To see the results in a browser, type: open /Users/2391266776qq.com/qc_singleSubj/index.html Done! To view results, run one of the following commands (depending on your preferred viewer): fslview_deprecated /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri/dmri_dwi_mean.nii.gz -l Greyscale /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri/dmri_dwi_mean_seg.nii.gz -l Red -t 0.7 & fslview /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri/dmri_dwi_mean.nii.gz -l Greyscale /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri/dmri_dwi_mean_seg.nii.gz -l Red -t 0.7 & 2391266776qq.com@ShydeMacBook-Pro dmri % sct_create_mask -i dmri_dwi_mean.nii.gz -p centerline,dmri_dwi_mean_seg.nii.gz -f cylinder -size 35mm -- Spinal Cord Toolbox (5.8) sct_create_mask -i dmri_dwi_mean.nii.gz -p centerline,dmri_dwi_mean_seg.nii.gz -f cylinder -size 35mm -- OK: dmri_dwi_mean_seg.nii.gz Creating temporary folder (/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321003052.413030-create_mask-rwfb_aj8) Orientation: RPI Dimensions: (256, 256, 25, 1, 0.7813, 0.7813, 4.000002, 1) Create mask... /Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/scripts/sct_create_mask.py:230: DeprecationWarning: get_header method is deprecated. Please use the ``img.header`` property instead. * deprecated from version: 2.1 * Will raise as of version: 4.0 hdr = centerline.get_header() # get header /Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/scripts/sct_create_mask.py:233: DeprecationWarning: get_data() is deprecated in favor of get_fdata(), which has a more predictable return type. To obtain get_data() behavior going forward, use numpy.asanyarray(img.dataobj). * deprecated from version: 3.0 * Will raise as of version: 5.0 data_centerline = centerline.get_data() # get centerline /Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/scripts/sct_create_mask.py:245: DeprecationWarning: Please use `center_of_mass` from the `scipy.ndimage` namespace, the `scipy.ndimage.measurements` namespace is deprecated. cx[iz], cy[iz] = ndimage.measurements.center_of_mass(np.array(data_centerline[:, :, iz])) Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'. Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'. Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'. Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'. Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'. Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'. Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'. Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'. Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'. Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'. Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'. Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'. Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'. Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'. Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'. Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'. Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'. Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'. Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'. Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'. Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'. Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'. Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'. Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'. Image header specifies datatype 'uint8', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'. Image header specifies datatype 'float64', but array is of type 'int64'. Header metadata will be overwritten to use 'int64'. Remove temporary files... rm -rf /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321003052.413030-create_mask-rwfb_aj8 Done! To view results, run one of the following commands (depending on your preferred viewer): fslview_deprecated /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri/dmri_dwi_mean.nii.gz -l Greyscale /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri/mask_dmri_dwi_mean.nii.gz -l Red -t 0.5 & fslview /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri/dmri_dwi_mean.nii.gz -l Greyscale /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri/mask_dmri_dwi_mean.nii.gz -l Red -t 0.5 & 2391266776qq.com@ShydeMacBook-Pro dmri % sct_dmri_moco -i dmri.nii.gz -m mask_dmri_dwi_mean.nii.gz -bvec dmri.bvec \ -qc ~/qc_singleSubj -qc-seg dmri_dwi_mean_seg.nii.gz -- Spinal Cord Toolbox (5.8) sct_dmri_moco -i dmri.nii.gz -m mask_dmri_dwi_mean.nii.gz -bvec dmri.bvec -qc /Users/2391266776qq.com/qc_singleSubj -qc-seg dmri_dwi_mean_seg.nii.gz -- Input parameters: Input file ............ dmri.nii.gz Group size ............ 3 Creating temporary folder (/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321003629.150640-moco-qbnmsmse) Copying input data to tmp folder and convert to nii... Get dimensions of data... 256 x 256 x 25 Data orientation: RPI Treated as axial Set suffix of transformation file name, which depends on the orientation: Orientation is axial, suffix is 'Warp.nii.gz'. The estimated transformation is a 3D warping field, which is composed of a stack of 2D Tx-Ty transformations Identify b=0 and DWI images... WARNING: bvecs file is 3xn instead of nx3. Consider using sct_dmri_transpose_bvecs. Transpose bvecs... Number of b=0: 1 [0] Number of DWI: 12 [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12] Split along T dimension... Merge and average b=0 data... Image header specifies datatype 'int16', but array is of type 'float64'. Header metadata will be overwritten to use 'float64'. Merge within groups: 0%| | 0/4 [00:00 Saving gif /Users/2391266776qq.com/qc_singleSubj/single_subject/data/dmri/sct_dmri_moco/2023_03_21_003834.798500/overlay_img.gif Animation.save using Successfully generated the QC results in /Users/2391266776qq.com/qc_singleSubj/_json/qc_2023_03_21_003834.798500.json To see the results in a browser, type: open /Users/2391266776qq.com/qc_singleSubj/index.html Done! To view results, run one of the following commands (depending on your preferred viewer): fslview_deprecated -m ortho,ortho dmri_moco.nii.gz dmri.nii.gz & fslview -m ortho,ortho dmri_moco.nii.gz dmri.nii.gz & 2391266776qq.com@ShydeMacBook-Pro dmri % sct_deepseg_sc -i dmri_moco_dwi_mean.nii.gz -c dwi -qc ~/qc_singleSubj -- Spinal Cord Toolbox (5.8) sct_deepseg_sc -i dmri_moco_dwi_mean.nii.gz -c dwi -qc /Users/2391266776qq.com/qc_singleSubj -- Config deepseg_sc: Centerline algorithm: svm Brain in image: False Kernel dimension: 2d Contrast: dwi Threshold: 0.01 Creating temporary folder (/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321003953.933459-60m5ae2e) Reorient the image to RPI, if necessary... Finding the spinal cord centerline... Creating temporary folder (/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321003954.918653-qlovue2v) Remove temporary files... rm -rf /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321003954.918653-qlovue2v Cropping the image around the spinal cord... Normalizing the intensity... Segmenting the spinal cord using deep learning on 2D patches... Reassembling the image... Resampling the segmentation to the native image resolution using linear interpolation... Binarizing the resampled segmentation... Image header specifies datatype 'float32', but array is of type 'uint8'. Header metadata will be overwritten to use 'uint8'. Compute shape analysis: 100%|################| 25/25 [00:00<00:00, 317.14iter/s] Remove temporary files... rm -rf /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321003953.933459-60m5ae2e *** 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/2391266776qq.com/qc_singleSubj/single_subject/data/dmri/sct_deepseg_sc/2023_03_21_003957.626986/bkg_img.png Successfully generated the QC results in /Users/2391266776qq.com/qc_singleSubj/_json/qc_2023_03_21_003957.626986.json To see the results in a browser, type: open /Users/2391266776qq.com/qc_singleSubj/index.html Done! To view results, run one of the following commands (depending on your preferred viewer): fslview_deprecated /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri/dmri_moco_dwi_mean.nii.gz -l Greyscale /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri/dmri_moco_dwi_mean_seg.nii.gz -l Red -t 0.7 & fslview /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri/dmri_moco_dwi_mean.nii.gz -l Greyscale /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri/dmri_moco_dwi_mean_seg.nii.gz -l Red -t 0.7 & 2391266776qq.com@ShydeMacBook-Pro dmri % sct_register_multimodal -i "${SCT_DIR}/data/PAM50/template/PAM50_t1.nii.gz" \ -iseg "${SCT_DIR}/data/PAM50/template/PAM50_cord.nii.gz" \ -d dmri_moco_dwi_mean.nii.gz \ -dseg dmri_moco_dwi_mean_seg.nii.gz \ -initwarp ../t2/warp_template2anat.nii.gz \ -initwarpinv ../t2/warp_anat2template.nii.gz \ -owarp warp_template2dmri.nii.gz \ -owarpinv warp_dmri2template.nii.gz \ -param step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3 \ -qc ~/qc_singleSubj -- Spinal Cord Toolbox (5.8) sct_register_multimodal -i /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_t1.nii.gz -iseg /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_cord.nii.gz -d dmri_moco_dwi_mean.nii.gz -dseg dmri_moco_dwi_mean_seg.nii.gz -initwarp ../t2/warp_template2anat.nii.gz -initwarpinv ../t2/warp_anat2template.nii.gz -owarp warp_template2dmri.nii.gz -owarpinv warp_dmri2template.nii.gz -param step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3 -qc /Users/2391266776qq.com/qc_singleSubj -- Input parameters: Source .............. /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_t1.nii.gz (141, 141, 991) Destination ......... dmri_moco_dwi_mean.nii.gz (256, 256, 25) Init transfo ........ /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2/warp_template2anat.nii.gz Mask ................ Output name ......... Remove temp files ... 1 Verbose ............. 1 Check if input data are 3D... Creating temporary folder (/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321004705.800215-register-r1f7rptn) Copying input data to tmp folder and convert to nii... Skip step=0 and replace with initial transformations: /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2/warp_template2anat.nii.gz -- ESTIMATE TRANSFORMATION FOR STEP #1 Apply transformation from previous step /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i src_seg.nii -o src_seg_reg.nii -t /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2/warp_template2anat.nii.gz -r dest_seg_RPI.nii -n NearestNeighbor # in /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321004705.800215-register-r1f7rptn 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/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321004707.253004-register-hi4ewskj) Copy input data to temp folder... Get image dimensions of destination image... matrix size: 256 x 256 x 25 voxel size: 0.7813mm x 0.7813mm x 25mm Split input segmentation... Split destination segmentation... Estimate cord angle for each slice: 0%| | 0/25 [00:00 step1Warp.nii.gz Generate warping field... --> step1InverseWarp.nii.gz Move warping fields... cp step1Warp.nii.gz /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321004705.800215-register-r1f7rptn cp step1InverseWarp.nii.gz /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321004705.800215-register-r1f7rptn rm -rf /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321004707.253004-register-hi4ewskj -- ESTIMATE TRANSFORMATION FOR STEP #2 Apply transformation from previous step /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i src_seg.nii -o src_seg_reg.nii -t warp_forward_1.nii.gz /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2/warp_template2anat.nii.gz -r dest_seg_RPI.nii -n NearestNeighbor # in /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321004705.800215-register-r1f7rptn Registration parameters: type ........... seg algo ........... bsplinesyn slicewise ...... 1 metric ......... MeanSquares samplStrategy .. None samplPercent ... 0.2 iter ........... 3 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/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321004711.721051-register-_sva8jsl) Copy input data to temp folder... Get image dimensions of destination image... matrix size: 256 x 256 x 25 voxel size: 0.7813mm x 0.7813mm x 25mm Split input volume... Split destination volume... Registering slice 0/24... /Users/2391266776qq.com/sct_5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0000.nii,src_Z0000.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0000,src_Z0000_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321004711.721051-register-_sva8jsl Registering slice 1/24... /Users/2391266776qq.com/sct_5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0001.nii,src_Z0001.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0001,src_Z0001_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321004711.721051-register-_sva8jsl Registering slice 2/24... /Users/2391266776qq.com/sct_5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0002.nii,src_Z0002.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0002,src_Z0002_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321004711.721051-register-_sva8jsl Registering slice 3/24... /Users/2391266776qq.com/sct_5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0003.nii,src_Z0003.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0003,src_Z0003_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321004711.721051-register-_sva8jsl Registering slice 4/24... /Users/2391266776qq.com/sct_5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0004.nii,src_Z0004.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0004,src_Z0004_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321004711.721051-register-_sva8jsl Registering slice 5/24... /Users/2391266776qq.com/sct_5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0005.nii,src_Z0005.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0005,src_Z0005_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321004711.721051-register-_sva8jsl Registering slice 6/24... /Users/2391266776qq.com/sct_5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0006.nii,src_Z0006.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0006,src_Z0006_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321004711.721051-register-_sva8jsl Registering slice 7/24... /Users/2391266776qq.com/sct_5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0007.nii,src_Z0007.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0007,src_Z0007_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321004711.721051-register-_sva8jsl Registering slice 8/24... /Users/2391266776qq.com/sct_5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0008.nii,src_Z0008.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0008,src_Z0008_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321004711.721051-register-_sva8jsl Registering slice 9/24... /Users/2391266776qq.com/sct_5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0009.nii,src_Z0009.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0009,src_Z0009_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321004711.721051-register-_sva8jsl Registering slice 10/24... /Users/2391266776qq.com/sct_5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0010.nii,src_Z0010.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0010,src_Z0010_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321004711.721051-register-_sva8jsl Registering slice 11/24... /Users/2391266776qq.com/sct_5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0011.nii,src_Z0011.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0011,src_Z0011_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321004711.721051-register-_sva8jsl Registering slice 12/24... /Users/2391266776qq.com/sct_5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0012.nii,src_Z0012.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0012,src_Z0012_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321004711.721051-register-_sva8jsl Registering slice 13/24... /Users/2391266776qq.com/sct_5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0013.nii,src_Z0013.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0013,src_Z0013_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321004711.721051-register-_sva8jsl Registering slice 14/24... /Users/2391266776qq.com/sct_5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0014.nii,src_Z0014.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0014,src_Z0014_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321004711.721051-register-_sva8jsl Registering slice 15/24... /Users/2391266776qq.com/sct_5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0015.nii,src_Z0015.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0015,src_Z0015_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321004711.721051-register-_sva8jsl Registering slice 16/24... /Users/2391266776qq.com/sct_5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0016.nii,src_Z0016.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0016,src_Z0016_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321004711.721051-register-_sva8jsl Registering slice 17/24... /Users/2391266776qq.com/sct_5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0017.nii,src_Z0017.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0017,src_Z0017_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321004711.721051-register-_sva8jsl Registering slice 18/24... /Users/2391266776qq.com/sct_5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0018.nii,src_Z0018.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0018,src_Z0018_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321004711.721051-register-_sva8jsl Registering slice 19/24... /Users/2391266776qq.com/sct_5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0019.nii,src_Z0019.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0019,src_Z0019_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321004711.721051-register-_sva8jsl Registering slice 20/24... /Users/2391266776qq.com/sct_5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0020.nii,src_Z0020.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0020,src_Z0020_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321004711.721051-register-_sva8jsl Registering slice 21/24... /Users/2391266776qq.com/sct_5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0021.nii,src_Z0021.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0021,src_Z0021_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321004711.721051-register-_sva8jsl Registering slice 22/24... /Users/2391266776qq.com/sct_5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0022.nii,src_Z0022.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0022,src_Z0022_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321004711.721051-register-_sva8jsl Registering slice 23/24... /Users/2391266776qq.com/sct_5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0023.nii,src_Z0023.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0023,src_Z0023_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321004711.721051-register-_sva8jsl Registering slice 24/24... /Users/2391266776qq.com/sct_5.8/bin/isct_antsRegistration --dimensionality 2 --transform 'BSplineSyN[0.5,1,3]' --metric 'MeanSquares[dest_Z0024.nii,src_Z0024.nii,1,4]' --convergence 3 --shrink-factors 1 --smoothing-sigmas 0mm --output '[warp2d_0024,src_Z0024_reg.nii]' --interpolation 'BSpline[3]' --verbose 1 # in /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321004711.721051-register-_sva8jsl Merge warping fields along z... Move warping fields... cp step2Warp.nii.gz /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321004705.800215-register-r1f7rptn cp step2InverseWarp.nii.gz /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321004705.800215-register-r1f7rptn rm -rf /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321004711.721051-register-_sva8jsl Concatenate transformations... /Users/2391266776qq.com/sct_5.8/bin/isct_ComposeMultiTransform 3 warp_src2dest.nii.gz -R dest.nii warp_forward_2.nii.gz warp_forward_1.nii.gz /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2/warp_template2anat.nii.gz # in /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321004705.800215-register-r1f7rptn /Users/2391266776qq.com/sct_5.8/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/t2/warp_anat2template.nii.gz warp_inverse_1.nii.gz warp_inverse_2.nii.gz # in /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321004705.800215-register-r1f7rptn Apply transfo source --> dest... /Users/2391266776qq.com/sct_5.8/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/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321004705.800215-register-r1f7rptn Apply transfo dest --> source... /Users/2391266776qq.com/sct_5.8/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/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321004705.800215-register-r1f7rptn Generate output files... File created: PAM50_t1_reg.nii.gz mv /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321004705.800215-register-r1f7rptn/warp_src2dest.nii.gz warp_template2dmri.nii.gz File created: warp_template2dmri.nii.gz File created: dmri_moco_dwi_mean_reg.nii.gz mv /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321004705.800215-register-r1f7rptn/warp_dest2src.nii.gz warp_dmri2template.nii.gz File created: warp_dmri2template.nii.gz Remove temporary files... rm -rf /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230321004705.800215-register-r1f7rptn Finished! Elapsed time: 37s *** 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/2391266776qq.com/qc_singleSubj/single_subject/data/dmri/sct_register_multimodal/2023_03_21_004744.303735/bkg_img.png Successfully generated the QC results in /Users/2391266776qq.com/qc_singleSubj/_json/qc_2023_03_21_004744.303735.json To see the results in a browser, type: open /Users/2391266776qq.com/qc_singleSubj/index.html Done! To view results, run one of the following commands (depending on your preferred viewer): fslview_deprecated /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_t1.nii.gz dmri_moco_dwi_mean_reg.nii.gz & fslview /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_t1.nii.gz dmri_moco_dwi_mean_reg.nii.gz & Done! To view results, run one of the following commands (depending on your preferred viewer): fslview_deprecated dmri_moco_dwi_mean.nii.gz PAM50_t1_reg.nii.gz & fslview dmri_moco_dwi_mean.nii.gz PAM50_t1_reg.nii.gz & 2391266776qq.com@ShydeMacBook-Pro dmri % sct_warp_template -d dmri_moco_dwi_mean.nii.gz -w warp_template2dmri.nii.gz -qc ~/qc_singleSubj -- Spinal Cord Toolbox (5.8) sct_warp_template -d dmri_moco_dwi_mean.nii.gz -w warp_template2dmri.nii.gz -qc /Users/2391266776qq.com/qc_singleSubj -- Check parameters: Working directory ........ /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri Destination image ........ dmri_moco_dwi_mean.nii.gz Warping field ............ warp_template2dmri.nii.gz Path template ............ /Users/2391266776qq.com/sct_5.8/data/PAM50 Output folder ............ label WARP TEMPLATE: /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_t1.nii.gz -o label/template/PAM50_t1.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_t2.nii.gz -o label/template/PAM50_t2.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_t2s.nii.gz -o label/template/PAM50_t2s.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_cord.nii.gz -o label/template/PAM50_cord.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n NearestNeighbor # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_wm.nii.gz -o label/template/PAM50_wm.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_gm.nii.gz -o label/template/PAM50_gm.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_csf.nii.gz -o label/template/PAM50_csf.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n NearestNeighbor # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_levels.nii.gz -o label/template/PAM50_levels.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n NearestNeighbor # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_levels_continuous.nii.gz -o label/template/PAM50_levels_continuous.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_label_body.nii.gz -o label/template/PAM50_label_body.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_label_disc.nii.gz -o label/template/PAM50_label_disc.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_label_discPosterior.nii.gz -o label/template/PAM50_label_discPosterior.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_spine.nii.gz -o label/template/PAM50_spine.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_centerline.nii.gz -o label/template/PAM50_centerline.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_label_spinal_levels.nii.gz -o label/template/PAM50_label_spinal_levels.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n NearestNeighbor # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri cp /Users/2391266776qq.com/sct_5.8/data/PAM50/template/info_label.txt label/template WARP ATLAS OF WHITE MATTER TRACTS: /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/atlas/PAM50_atlas_00.nii.gz -o label/atlas/PAM50_atlas_00.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/atlas/PAM50_atlas_01.nii.gz -o label/atlas/PAM50_atlas_01.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/atlas/PAM50_atlas_02.nii.gz -o label/atlas/PAM50_atlas_02.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/atlas/PAM50_atlas_03.nii.gz -o label/atlas/PAM50_atlas_03.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/atlas/PAM50_atlas_04.nii.gz -o label/atlas/PAM50_atlas_04.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/atlas/PAM50_atlas_05.nii.gz -o label/atlas/PAM50_atlas_05.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/atlas/PAM50_atlas_06.nii.gz -o label/atlas/PAM50_atlas_06.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/atlas/PAM50_atlas_07.nii.gz -o label/atlas/PAM50_atlas_07.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/atlas/PAM50_atlas_08.nii.gz -o label/atlas/PAM50_atlas_08.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/atlas/PAM50_atlas_09.nii.gz -o label/atlas/PAM50_atlas_09.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/atlas/PAM50_atlas_10.nii.gz -o label/atlas/PAM50_atlas_10.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/atlas/PAM50_atlas_11.nii.gz -o label/atlas/PAM50_atlas_11.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/atlas/PAM50_atlas_12.nii.gz -o label/atlas/PAM50_atlas_12.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/atlas/PAM50_atlas_13.nii.gz -o label/atlas/PAM50_atlas_13.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/atlas/PAM50_atlas_14.nii.gz -o label/atlas/PAM50_atlas_14.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/atlas/PAM50_atlas_15.nii.gz -o label/atlas/PAM50_atlas_15.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/atlas/PAM50_atlas_16.nii.gz -o label/atlas/PAM50_atlas_16.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/atlas/PAM50_atlas_17.nii.gz -o label/atlas/PAM50_atlas_17.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/atlas/PAM50_atlas_18.nii.gz -o label/atlas/PAM50_atlas_18.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/atlas/PAM50_atlas_19.nii.gz -o label/atlas/PAM50_atlas_19.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/atlas/PAM50_atlas_20.nii.gz -o label/atlas/PAM50_atlas_20.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/atlas/PAM50_atlas_21.nii.gz -o label/atlas/PAM50_atlas_21.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/atlas/PAM50_atlas_22.nii.gz -o label/atlas/PAM50_atlas_22.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/atlas/PAM50_atlas_23.nii.gz -o label/atlas/PAM50_atlas_23.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/atlas/PAM50_atlas_24.nii.gz -o label/atlas/PAM50_atlas_24.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/atlas/PAM50_atlas_25.nii.gz -o label/atlas/PAM50_atlas_25.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/atlas/PAM50_atlas_26.nii.gz -o label/atlas/PAM50_atlas_26.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/atlas/PAM50_atlas_27.nii.gz -o label/atlas/PAM50_atlas_27.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/atlas/PAM50_atlas_28.nii.gz -o label/atlas/PAM50_atlas_28.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/atlas/PAM50_atlas_29.nii.gz -o label/atlas/PAM50_atlas_29.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/atlas/PAM50_atlas_30.nii.gz -o label/atlas/PAM50_atlas_30.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/atlas/PAM50_atlas_31.nii.gz -o label/atlas/PAM50_atlas_31.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/atlas/PAM50_atlas_32.nii.gz -o label/atlas/PAM50_atlas_32.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/atlas/PAM50_atlas_33.nii.gz -o label/atlas/PAM50_atlas_33.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/atlas/PAM50_atlas_34.nii.gz -o label/atlas/PAM50_atlas_34.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/atlas/PAM50_atlas_35.nii.gz -o label/atlas/PAM50_atlas_35.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri /Users/2391266776qq.com/sct_5.8/bin/isct_antsApplyTransforms -d 3 -i /Users/2391266776qq.com/sct_5.8/data/PAM50/atlas/PAM50_atlas_36.nii.gz -o label/atlas/PAM50_atlas_36.nii.gz -t warp_template2dmri.nii.gz -r dmri_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM-SCT/single_subject/data/dmri cp /Users/2391266776qq.com/sct_5.8/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/2391266776qq.com/sct_5.8/python/envs/venv_sct/lib/python3.8/site-packages/scipy/ndimage/_measurements.py:1407: RuntimeWarning: invalid value encountered in double_scalars results = [sum(input * grids[dir].astype(float), labels, index) / normalizer /Users/2391266776qq.com/qc_singleSubj/single_subject/data/dmri/sct_warp_template/2023_03_21_005052.108025/bkg_img.png Successfully generated the QC results in /Users/2391266776qq.com/qc_singleSubj/_json/qc_2023_03_21_005052.108025.json To see the results in a browser, type: open /Users/2391266776qq.com/qc_singleSubj/index.html Done! To view results, run one of the following commands (depending on your preferred viewer): fslview_deprecated dmri_moco_dwi_mean.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 dmri_moco_dwi_mean.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 & 2391266776qq.com@ShydeMacBook-Pro dmri % sct_dmri_compute_dti -i dmri_moco.nii.gz -bval dmri.bval -bvec dmri.bvec -- Spinal Cord Toolbox (5.8) sct_dmri_compute_dti -i dmri_moco.nii.gz -bval dmri.bval -bvec dmri.bvec -- data.shape (256, 256, 25, 13) Computing tensor using "standard" method... Computing metrics... 2391266776qq.com@ShydeMacBook-Pro dmri % sct_extract_metric -i dti_FA.nii.gz -f label/atlas \ -l 51 -method map \ -vert 3:7 -vertfile label/template/PAM50_levels.nii.gz -perlevel 1 \ -o fa_in_wm.csv -- Spinal Cord Toolbox (5.8) sct_extract_metric -i dti_FA.nii.gz -f label/atlas -l 51 -method map -vert 3:7 -vertfile label/template/PAM50_levels.nii.gz -perlevel 1 -o fa_in_wm.csv -- Load metric image... Estimation for label: white matter Done! To view results, type: open fa_in_wm.csv 2391266776qq.com@ShydeMacBook-Pro dmri % sct_extract_metric -i dti_FA.nii.gz -f label/atlas \ -l 51 -method map \ -disc 3:7 -discfile label/template/PAM50_levels.nii.gz -perlevel 1 \ -o fa_in_wm.csv -- Spinal Cord Toolbox (5.8) sct_extract_metric -i dti_FA.nii.gz -f label/atlas -l 51 -method map -disc 3:7 -discfile label/template/PAM50_levels.nii.gz -perlevel 1 -o fa_in_wm.csv -- usage: sct_extract_metric -i [-h] [-f ] [-l ] [-list-labels] [-method {ml,map,wa,bin,median,max}] [-append {0,1}] [-combine {0,1}] [-o ] [-output-map ] [-z ] [-perslice {0,1}] [-vert ] [-vertfile ] [-perlevel ] [-v ] [-param ] [-fix-label ] [-norm-file ] [-norm-method {sbs,whole}] [-mask-weighted ] [-discard-neg-val {0,1}] This program extracts metrics (e.g., DTI or MTR) within labels. Labels could be a single file or a folder generated with 'sct_warp_template' containing multiple label files and a label description file (info_label.txt). The labels should be in the same space coordinates as the input image. The labels used by default are taken from the PAM50 template. To learn about the available PAM50 white/grey matter atlas labels and their corresponding ID values, please refer to: https://spinalcordtoolbox.com/en/latest/overview/concepts/pam50.html#white-and- grey-matter-atlas-pam50-atlas To compute FA within labels 0, 2 and 3 within vertebral levels C2 to C7 using binary method: sct_extract_metric -i dti_FA.nii.gz -l 0,2,3 -vert 2:7 -method bin To compute average MTR in a region defined by a single label file (could be binary or 0-1 weighted mask) between slices 1 and 4: sct_extract_metric -i mtr.nii.gz -f my_mask.nii.gz -z 1:4 -method wa MANDATORY ARGUMENTS: -i Image file to extract metrics from. Example: FA.nii.gz OPTIONAL ARGUMENTS: -h, --help Show this help message and exit. -f Single label file, or folder that contains WM tract labels.Example: /Users/2391266776qq.com/sct_5.8/data/atlas (default: label/atlas) -l Label IDs to extract the metric from. Default = all labels. Separate labels with ','. To select a group of consecutive labels use ':'. Example: 1:3 is equivalent to 1,2,3. Maximum Likelihood (or MAP) is computed using all tracts, but only values of the selected tracts are reported. -list-labels List available labels. These labels are defined in the file 'info_label.txt' located in the folder specified by the flag '-f'. -method {ml,map,wa,bin,median,max} Method to extract metrics. - ml: maximum likelihood. This method is recommended for large labels and low noise. Also, this method should only be used with the PAM50 white/gray matter atlas, or with any custom atlas as long as the sum across all labels equals 1, in each voxel part of the atlas. - map: maximum a posteriori. Mean priors are estimated by maximum likelihood within three clusters (white matter, gray matter and CSF). Tract and noise variance are set with flag -p. This method should only be used with the PAM50 white/gray matter atlas, or with any custom atlas as long as the sum across all labels equals 1, in each voxel part of the atlas. - wa: weighted average - bin: binarize mask (threshold=0.5) - median: weighted median. This implementation of the median treats quantiles as a continuous (vs. discrete) function. For more details, see https://pypi.org/project/wquantiles/. - max: for each z-slice of the input data, extract the max value for each slice of the input data. (default: wa) -append {0,1} Whether to append results as a new line in the output csv file instead of overwriting it. 0 = no, 1 = yes (default: 0) -combine {0,1} Whether to combine multiple labels into a single estimation. 0 = no, 1 = yes (default: 0) -o File name of the output result file collecting the metric estimation results. Include the '.csv' file extension in the file name. Example: extract_metric.csv (default: extract_metric.csv) -output-map File name for an image consisting of the atlas labels multiplied by the estimated metric values yielding the metric value map, useful to assess the metric estimation and especially partial volume effects. -z Slice range to estimate the metric from. First slice is 0. Example: 5:23 You can also select specific slices using commas. Example: 0,2,3,5,12' -perslice {0,1} Whether to output one metric per slice instead of a single output metric. 0 = no, 1 = yes. Please note that when methods ml or map are used, outputting a single metric per slice and then averaging them all is not the same as outputting a single metric at once across all slices. -vert Vertebral levels to compute the metrics across. Example: 2:9 for C2 to T2. If you also specify a range of slices with flag `-z`, the intersection between the specified slices and vertebral levels will be considered. -vertfile Vertebral labeling file. Only use with flag -vert. The input Image and the vertebral labelling file must in the same voxel coordinate system and must match the dimensions between each other. (default: ./label/template/PAM50_levels.nii.gz) -perlevel Whether to output one metric per vertebral level instead of a single output metric. 0 = no, 1 = yes. Please note that this flag needs to be used with the -vert option. (default: 0) -v Verbosity. 0: Display only errors/warnings, 1: Errors/warnings + info messages, 2: Debug mode (default: 1) FOR ADVANCED USERS: -param Advanced parameters for the 'map' method. Separate with comma. All items must be listed (separated with comma). - #1: standard deviation of metrics across labels - #2: standard deviation of the noise (assumed Gaussian) -fix-label When using ML or MAP estimations, if you do not want to estimate the metric in one label and fix its value to avoid effects on other labels, specify , Filename of the label by which the user wants to normalize. -norm-method {sbs,whole} Method to use for normalization: - sbs: normalization slice-by-slice - whole: normalization by the metric value in the whole label for all slices. -mask-weighted Nifti mask to weight each voxel during ML or MAP estimation. Example: PAM50_wm.nii.gz -discard-neg-val {0,1} Whether to discard voxels with negative value when computing metrics statistics. 0 = no, 1 = yes (default: 0) sct_extract_metric: error: argument -discard-neg-val: invalid choice: '3:7' (choose from '0', '1') 2391266776qq.com@ShydeMacBook-Pro dmri % sct_extract_metric -i dti_FA.nii.gz -f label/atlas \ -l 51 -method map \ -disc 3,4,5,6,7 -discfile label/template/PAM50_levels.nii.gz -perlevel 1 \ -o fa_in_wm.csv -- Spinal Cord Toolbox (5.8) sct_extract_metric -i dti_FA.nii.gz -f label/atlas -l 51 -method map -disc 3,4,5,6,7 -discfile label/template/PAM50_levels.nii.gz -perlevel 1 -o fa_in_wm.csv -- usage: sct_extract_metric -i [-h] [-f ] [-l ] [-list-labels] [-method {ml,map,wa,bin,median,max}] [-append {0,1}] [-combine {0,1}] [-o ] [-output-map ] [-z ] [-perslice {0,1}] [-vert ] [-vertfile ] [-perlevel ] [-v ] [-param ] [-fix-label ] [-norm-file ] [-norm-method {sbs,whole}] [-mask-weighted ] [-discard-neg-val {0,1}] This program extracts metrics (e.g., DTI or MTR) within labels. Labels could be a single file or a folder generated with 'sct_warp_template' containing multiple label files and a label description file (info_label.txt). The labels should be in the same space coordinates as the input image. The labels used by default are taken from the PAM50 template. To learn about the available PAM50 white/grey matter atlas labels and their corresponding ID values, please refer to: https://spinalcordtoolbox.com/en/latest/overview/concepts/pam50.html#white-and- grey-matter-atlas-pam50-atlas To compute FA within labels 0, 2 and 3 within vertebral levels C2 to C7 using binary method: sct_extract_metric -i dti_FA.nii.gz -l 0,2,3 -vert 2:7 -method bin To compute average MTR in a region defined by a single label file (could be binary or 0-1 weighted mask) between slices 1 and 4: sct_extract_metric -i mtr.nii.gz -f my_mask.nii.gz -z 1:4 -method wa MANDATORY ARGUMENTS: -i Image file to extract metrics from. Example: FA.nii.gz OPTIONAL ARGUMENTS: -h, --help Show this help message and exit. -f Single label file, or folder that contains WM tract labels.Example: /Users/2391266776qq.com/sct_5.8/data/atlas (default: label/atlas) -l Label IDs to extract the metric from. Default = all labels. Separate labels with ','. To select a group of consecutive labels use ':'. Example: 1:3 is equivalent to 1,2,3. Maximum Likelihood (or MAP) is computed using all tracts, but only values of the selected tracts are reported. -list-labels List available labels. These labels are defined in the file 'info_label.txt' located in the folder specified by the flag '-f'. -method {ml,map,wa,bin,median,max} Method to extract metrics. - ml: maximum likelihood. This method is recommended for large labels and low noise. Also, this method should only be used with the PAM50 white/gray matter atlas, or with any custom atlas as long as the sum across all labels equals 1, in each voxel part of the atlas. - map: maximum a posteriori. Mean priors are estimated by maximum likelihood within three clusters (white matter, gray matter and CSF). Tract and noise variance are set with flag -p. This method should only be used with the PAM50 white/gray matter atlas, or with any custom atlas as long as the sum across all labels equals 1, in each voxel part of the atlas. - wa: weighted average - bin: binarize mask (threshold=0.5) - median: weighted median. This implementation of the median treats quantiles as a continuous (vs. discrete) function. For more details, see https://pypi.org/project/wquantiles/. - max: for each z-slice of the input data, extract the max value for each slice of the input data. (default: wa) -append {0,1} Whether to append results as a new line in the output csv file instead of overwriting it. 0 = no, 1 = yes (default: 0) -combine {0,1} Whether to combine multiple labels into a single estimation. 0 = no, 1 = yes (default: 0) -o File name of the output result file collecting the metric estimation results. Include the '.csv' file extension in the file name. Example: extract_metric.csv (default: extract_metric.csv) -output-map File name for an image consisting of the atlas labels multiplied by the estimated metric values yielding the metric value map, useful to assess the metric estimation and especially partial volume effects. -z Slice range to estimate the metric from. First slice is 0. Example: 5:23 You can also select specific slices using commas. Example: 0,2,3,5,12' -perslice {0,1} Whether to output one metric per slice instead of a single output metric. 0 = no, 1 = yes. Please note that when methods ml or map are used, outputting a single metric per slice and then averaging them all is not the same as outputting a single metric at once across all slices. -vert Vertebral levels to compute the metrics across. Example: 2:9 for C2 to T2. If you also specify a range of slices with flag `-z`, the intersection between the specified slices and vertebral levels will be considered. -vertfile Vertebral labeling file. Only use with flag -vert. The input Image and the vertebral labelling file must in the same voxel coordinate system and must match the dimensions between each other. (default: ./label/template/PAM50_levels.nii.gz) -perlevel Whether to output one metric per vertebral level instead of a single output metric. 0 = no, 1 = yes. Please note that this flag needs to be used with the -vert option. (default: 0) -v Verbosity. 0: Display only errors/warnings, 1: Errors/warnings + info messages, 2: Debug mode (default: 1) FOR ADVANCED USERS: -param Advanced parameters for the 'map' method. Separate with comma. All items must be listed (separated with comma). - #1: standard deviation of metrics across labels - #2: standard deviation of the noise (assumed Gaussian) -fix-label When using ML or MAP estimations, if you do not want to estimate the metric in one label and fix its value to avoid effects on other labels, specify , Filename of the label by which the user wants to normalize. -norm-method {sbs,whole} Method to use for normalization: - sbs: normalization slice-by-slice - whole: normalization by the metric value in the whole label for all slices. -mask-weighted Nifti mask to weight each voxel during ML or MAP estimation. Example: PAM50_wm.nii.gz -discard-neg-val {0,1} Whether to discard voxels with negative value when computing metrics statistics. 0 = no, 1 = yes (default: 0) sct_extract_metric: error: argument -discard-neg-val: invalid choice: '3,4,5,6,7' (choose from '0', '1') 2391266776qq.com@ShydeMacBook-Pro dmri % sct_extract_metric -i dti_FA.nii.gz -f label/atlas \ -l 51 -method map \ -disc '3','4','5','6','7' -discfile label/template/PAM50_levels.nii.gz -perlevel 1 \ -o fa_in_wm.csv -- Spinal Cord Toolbox (5.8) sct_extract_metric -i dti_FA.nii.gz -f label/atlas -l 51 -method map -disc 3,4,5,6,7 -discfile label/template/PAM50_levels.nii.gz -perlevel 1 -o fa_in_wm.csv -- usage: sct_extract_metric -i [-h] [-f ] [-l ] [-list-labels] [-method {ml,map,wa,bin,median,max}] [-append {0,1}] [-combine {0,1}] [-o ] [-output-map ] [-z ] [-perslice {0,1}] [-vert ] [-vertfile ] [-perlevel ] [-v ] [-param ] [-fix-label ] [-norm-file ] [-norm-method {sbs,whole}] [-mask-weighted ] [-discard-neg-val {0,1}] This program extracts metrics (e.g., DTI or MTR) within labels. Labels could be a single file or a folder generated with 'sct_warp_template' containing multiple label files and a label description file (info_label.txt). The labels should be in the same space coordinates as the input image. The labels used by default are taken from the PAM50 template. To learn about the available PAM50 white/grey matter atlas labels and their corresponding ID values, please refer to: https://spinalcordtoolbox.com/en/latest/overview/concepts/pam50.html#white-and- grey-matter-atlas-pam50-atlas To compute FA within labels 0, 2 and 3 within vertebral levels C2 to C7 using binary method: sct_extract_metric -i dti_FA.nii.gz -l 0,2,3 -vert 2:7 -method bin To compute average MTR in a region defined by a single label file (could be binary or 0-1 weighted mask) between slices 1 and 4: sct_extract_metric -i mtr.nii.gz -f my_mask.nii.gz -z 1:4 -method wa MANDATORY ARGUMENTS: -i Image file to extract metrics from. Example: FA.nii.gz OPTIONAL ARGUMENTS: -h, --help Show this help message and exit. -f Single label file, or folder that contains WM tract labels.Example: /Users/2391266776qq.com/sct_5.8/data/atlas (default: label/atlas) -l Label IDs to extract the metric from. Default = all labels. Separate labels with ','. To select a group of consecutive labels use ':'. Example: 1:3 is equivalent to 1,2,3. Maximum Likelihood (or MAP) is computed using all tracts, but only values of the selected tracts are reported. -list-labels List available labels. These labels are defined in the file 'info_label.txt' located in the folder specified by the flag '-f'. -method {ml,map,wa,bin,median,max} Method to extract metrics. - ml: maximum likelihood. This method is recommended for large labels and low noise. Also, this method should only be used with the PAM50 white/gray matter atlas, or with any custom atlas as long as the sum across all labels equals 1, in each voxel part of the atlas. - map: maximum a posteriori. Mean priors are estimated by maximum likelihood within three clusters (white matter, gray matter and CSF). Tract and noise variance are set with flag -p. This method should only be used with the PAM50 white/gray matter atlas, or with any custom atlas as long as the sum across all labels equals 1, in each voxel part of the atlas. - wa: weighted average - bin: binarize mask (threshold=0.5) - median: weighted median. This implementation of the median treats quantiles as a continuous (vs. discrete) function. For more details, see https://pypi.org/project/wquantiles/. - max: for each z-slice of the input data, extract the max value for each slice of the input data. (default: wa) -append {0,1} Whether to append results as a new line in the output csv file instead of overwriting it. 0 = no, 1 = yes (default: 0) -combine {0,1} Whether to combine multiple labels into a single estimation. 0 = no, 1 = yes (default: 0) -o File name of the output result file collecting the metric estimation results. Include the '.csv' file extension in the file name. Example: extract_metric.csv (default: extract_metric.csv) -output-map File name for an image consisting of the atlas labels multiplied by the estimated metric values yielding the metric value map, useful to assess the metric estimation and especially partial volume effects. -z Slice range to estimate the metric from. First slice is 0. Example: 5:23 You can also select specific slices using commas. Example: 0,2,3,5,12' -perslice {0,1} Whether to output one metric per slice instead of a single output metric. 0 = no, 1 = yes. Please note that when methods ml or map are used, outputting a single metric per slice and then averaging them all is not the same as outputting a single metric at once across all slices. -vert Vertebral levels to compute the metrics across. Example: 2:9 for C2 to T2. If you also specify a range of slices with flag `-z`, the intersection between the specified slices and vertebral levels will be considered. -vertfile Vertebral labeling file. Only use with flag -vert. The input Image and the vertebral labelling file must in the same voxel coordinate system and must match the dimensions between each other. (default: ./label/template/PAM50_levels.nii.gz) -perlevel Whether to output one metric per vertebral level instead of a single output metric. 0 = no, 1 = yes. Please note that this flag needs to be used with the -vert option. (default: 0) -v Verbosity. 0: Display only errors/warnings, 1: Errors/warnings + info messages, 2: Debug mode (default: 1) FOR ADVANCED USERS: -param Advanced parameters for the 'map' method. Separate with comma. All items must be listed (separated with comma). - #1: standard deviation of metrics across labels - #2: standard deviation of the noise (assumed Gaussian) -fix-label When using ML or MAP estimations, if you do not want to estimate the metric in one label and fix its value to avoid effects on other labels, specify , Filename of the label by which the user wants to normalize. -norm-method {sbs,whole} Method to use for normalization: - sbs: normalization slice-by-slice - whole: normalization by the metric value in the whole label for all slices. -mask-weighted Nifti mask to weight each voxel during ML or MAP estimation. Example: PAM50_wm.nii.gz -discard-neg-val {0,1} Whether to discard voxels with negative value when computing metrics statistics. 0 = no, 1 = yes (default: 0) sct_extract_metric: error: argument -discard-neg-val: invalid choice: '3,4,5,6,7' (choose from '0', '1') 2391266776qq.com@ShydeMacBook-Pro dmri % sct_extract_metric -i dti_FA.nii.gz -f label/atlas \ -l 51 -method map \ -vert 3:7 -vertfile label/template/PAM50_levels.nii.gz -perlevel 1 \ -o fa_in_wm.csv -- Spinal Cord Toolbox (5.8) sct_extract_metric -i dti_FA.nii.gz -f label/atlas -l 51 -method map -vert 3:7 -vertfile label/template/PAM50_levels.nii.gz -perlevel 1 -o fa_in_wm.csv -- Load metric image... Estimation for label: white matter Done! To view results, type: open fa_in_wm.csv 2391266776qq.com@ShydeMacBook-Pro dmri % sct_extract_metric -i dti_AD.nii.gz -f label/atlas \ -l 51 -method map \ -vert 3:7 -vertfile label/template/PAM50_levels.nii.gz -perlevel 1 \ -o ad_in_wm.csv -- Spinal Cord Toolbox (5.8) sct_extract_metric -i dti_AD.nii.gz -f label/atlas -l 51 -method map -vert 3:7 -vertfile label/template/PAM50_levels.nii.gz -perlevel 1 -o ad_in_wm.csv -- Load metric image... Estimation for label: white matter Done! To view results, type: open ad_in_wm.csv 2391266776qq.com@ShydeMacBook-Pro dmri % sct_extract_metric -i dti_RD.nii.gz -f label/atlas \ -l 51 -method map \ -vert 3:7 -vertfile label/template/PAM50_levels.nii.gz -perlevel 1 \ -o rd_in_wm.csv -- Spinal Cord Toolbox (5.8) sct_extract_metric -i dti_RD.nii.gz -f label/atlas -l 51 -method map -vert 3:7 -vertfile label/template/PAM50_levels.nii.gz -perlevel 1 -o rd_in_wm.csv -- Load metric image... Estimation for label: white matter Done! To view results, type: open rd_in_wm.csv 2391266776qq.com@ShydeMacBook-Pro dmri % sct_extract_metric -i dti_MD.nii.gz -f label/atlas \ -l 51 -method map \ -vert 3:7 -vertfile label/template/PAM50_levels.nii.gz -perlevel 1 \ -o md_in_wm.csv -- Spinal Cord Toolbox (5.8) sct_extract_metric -i dti_MD.nii.gz -f label/atlas -l 51 -method map -vert 3:7 -vertfile label/template/PAM50_levels.nii.gz -perlevel 1 -o md_in_wm.csv -- Load metric image... Estimation for label: white matter Done! To view results, type: open md_in_wm.csv 2391266776qq.com@ShydeMacBook-Pro dmri %