Last login: Fri Feb 3 18:32:17 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 ~ % cd KINGSTON/CSM/data/museDTI/ cd: no such file or directory: KINGSTON/CSM/data/museDTI/ 2391266776qq.com@ShydeMacBook-Pro ~ % ls Applications Parallels Desktop Pictures Documents Public Downloads Zotero Library iCloud云盘（归档） Movies qc_singleSubj Music sct_5.8 2391266776qq.com@ShydeMacBook-Pro ~ % cd KINGSTON cd: no such file or directory: KINGSTON 2391266776qq.com@ShydeMacBook-Pro ~ % cd 2391266776qq.com@ShydeMacBook-Pro ~ % ls Applications Parallels Desktop Pictures Documents Public Downloads Zotero Library iCloud云盘（归档） Movies qc_singleSubj Music sct_5.8 2391266776qq.com@ShydeMacBook-Pro ~ % cd Documents 2391266776qq.com@ShydeMacBook-Pro Documents % ls IBM MATLAB SlicerDICOMDatabase 2391266776qq.com@ShydeMacBook-Pro Documents % cd .. 2391266776qq.com@ShydeMacBook-Pro ~ % ls Applications Parallels Desktop Pictures Documents Public Downloads Zotero Library iCloud云盘（归档） Movies qc_singleSubj Music sct_5.8 2391266776qq.com@ShydeMacBook-Pro ~ % cd qc_singleSubj 2391266776qq.com@ShydeMacBook-Pro qc_singleSubj % ls _assets _json index.html single_subject 2391266776qq.com@ShydeMacBook-Pro qc_singleSubj % 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 2391266776qq.com@ShydeMacBook-Pro data % cd dmri 2391266776qq.com@ShydeMacBook-Pro dmri % ls sct_deepseg_sc sct_register_multimodal sct_dmri_moco sct_warp_template 2391266776qq.com@ShydeMacBook-Pro dmri % cd ../.. 2391266776qq.com@ShydeMacBook-Pro single_subject % ls data 2391266776qq.com@ShydeMacBook-Pro single_subject % cd ../.. 2391266776qq.com@ShydeMacBook-Pro ~ % ls Applications Parallels Desktop Pictures Documents Public Downloads Zotero Library iCloud云盘（归档） Movies qc_singleSubj Music sct_5.8 2391266776qq.com@ShydeMacBook-Pro ~ % cd Downloads/CSM/data/museDTI/ 2391266776qq.com@ShydeMacBook-Pro museDTI % ls 0001.dcm 0061.dcm 0121.dcm 0181.dcm 0241.dcm 0002.dcm 0062.dcm 0122.dcm 0182.dcm 0242.dcm 0003.dcm 0063.dcm 0123.dcm 0183.dcm 0243.dcm 0004.dcm 0064.dcm 0124.dcm 0184.dcm 0244.dcm 0005.dcm 0065.dcm 0125.dcm 0185.dcm 0245.dcm 0006.dcm 0066.dcm 0126.dcm 0186.dcm 0246.dcm 0007.dcm 0067.dcm 0127.dcm 0187.dcm 0247.dcm 0008.dcm 0068.dcm 0128.dcm 0188.dcm 0248.dcm 0009.dcm 0069.dcm 0129.dcm 0189.dcm 0249.dcm 0010.dcm 0070.dcm 0130.dcm 0190.dcm 0250.dcm 0011.dcm 0071.dcm 0131.dcm 0191.dcm 0251.dcm 0012.dcm 0072.dcm 0132.dcm 0192.dcm 0252.dcm 0013.dcm 0073.dcm 0133.dcm 0193.dcm 0253.dcm 0014.dcm 0074.dcm 0134.dcm 0194.dcm 0254.dcm 0015.dcm 0075.dcm 0135.dcm 0195.dcm 0255.dcm 0016.dcm 0076.dcm 0136.dcm 0196.dcm 0256.dcm 0017.dcm 0077.dcm 0137.dcm 0197.dcm 0257.dcm 0018.dcm 0078.dcm 0138.dcm 0198.dcm 0258.dcm 0019.dcm 0079.dcm 0139.dcm 0199.dcm 0259.dcm 0020.dcm 0080.dcm 0140.dcm 0200.dcm 0260.dcm 0021.dcm 0081.dcm 0141.dcm 0201.dcm 0261.dcm 0022.dcm 0082.dcm 0142.dcm 0202.dcm 0262.dcm 0023.dcm 0083.dcm 0143.dcm 0203.dcm 0263.dcm 0024.dcm 0084.dcm 0144.dcm 0204.dcm 0264.dcm 0025.dcm 0085.dcm 0145.dcm 0205.dcm 0265.dcm 0026.dcm 0086.dcm 0146.dcm 0206.dcm 0266.dcm 0027.dcm 0087.dcm 0147.dcm 0207.dcm 0267.dcm 0028.dcm 0088.dcm 0148.dcm 0208.dcm 0268.dcm 0029.dcm 0089.dcm 0149.dcm 0209.dcm 0269.dcm 0030.dcm 0090.dcm 0150.dcm 0210.dcm 0270.dcm 0031.dcm 0091.dcm 0151.dcm 0211.dcm 0271.dcm 0032.dcm 0092.dcm 0152.dcm 0212.dcm 0272.dcm 0033.dcm 0093.dcm 0153.dcm 0213.dcm 0273.dcm 0034.dcm 0094.dcm 0154.dcm 0214.dcm 0274.dcm 0035.dcm 0095.dcm 0155.dcm 0215.dcm 0275.dcm 0036.dcm 0096.dcm 0156.dcm 0216.dcm 0276.dcm 0037.dcm 0097.dcm 0157.dcm 0217.dcm 0277.dcm 0038.dcm 0098.dcm 0158.dcm 0218.dcm 0278.dcm 0039.dcm 0099.dcm 0159.dcm 0219.dcm 0279.dcm 0040.dcm 0100.dcm 0160.dcm 0220.dcm 0280.dcm 0041.dcm 0101.dcm 0161.dcm 0221.dcm 0281.dcm 0042.dcm 0102.dcm 0162.dcm 0222.dcm 0282.dcm 0043.dcm 0103.dcm 0163.dcm 0223.dcm 0283.dcm 0044.dcm 0104.dcm 0164.dcm 0224.dcm 0284.dcm 0045.dcm 0105.dcm 0165.dcm 0225.dcm 0285.dcm 0046.dcm 0106.dcm 0166.dcm 0226.dcm 0286.dcm 0047.dcm 0107.dcm 0167.dcm 0227.dcm 0287.dcm 0048.dcm 0108.dcm 0168.dcm 0228.dcm 0288.dcm 0049.dcm 0109.dcm 0169.dcm 0229.dcm 0289.dcm 0050.dcm 0110.dcm 0170.dcm 0230.dcm 0290.dcm 0051.dcm 0111.dcm 0171.dcm 0231.dcm 0291.dcm 0052.dcm 0112.dcm 0172.dcm 0232.dcm 0292.dcm 0053.dcm 0113.dcm 0173.dcm 0233.dcm 0293.dcm 0054.dcm 0114.dcm 0174.dcm 0234.dcm 0294.dcm 0055.dcm 0115.dcm 0175.dcm 0235.dcm 0295.dcm 0056.dcm 0116.dcm 0176.dcm 0236.dcm 0296.dcm 0057.dcm 0117.dcm 0177.dcm 0237.dcm 0297.dcm 0058.dcm 0118.dcm 0178.dcm 0238.dcm 0298.dcm 0059.dcm 0119.dcm 0179.dcm 0239.dcm 0299.dcm 0060.dcm 0120.dcm 0180.dcm 0240.dcm 2391266776qq.com@ShydeMacBook-Pro museDTI % cd .. 2391266776qq.com@ShydeMacBook-Pro data % ls museDTI t2s 2391266776qq.com@ShydeMacBook-Pro data % ls museDTI t2s 2391266776qq.com@ShydeMacBook-Pro data % sct_dmri_separate_b0_and_dwi -i museDTI.nii.gz -bvec bvecs.txt -- Spinal Cord Toolbox (5.8) sct_dmri_separate_b0_and_dwi -i museDTI.nii.gz -bvec bvecs.txt -- Input parameters: input file ............museDTI.nii.gz bvecs file ............bvecs.txt bvals file ............ average ...............1 Creating temporary folder (/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230205101712.734010-dmri_separate-e2s1yy6i) Copy files into temporary folder... 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/data/museDTI.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_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 162, in main im_dmri = convert(Image(fname_data)) 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/data/museDTI.nii.gz' 2391266776qq.com@ShydeMacBook-Pro data % ls museDTI t2s 2391266776qq.com@ShydeMacBook-Pro data % cd museDTI 2391266776qq.com@ShydeMacBook-Pro museDTI % ls DTI museDTI.bval museDTI.bvec museDTI.json museDTI.nii.gz 2391266776qq.com@ShydeMacBook-Pro museDTI % sct_dmri_separate_b0_and_dwi -i museDTI.nii.gz -bvec bvecs.txt -- Spinal Cord Toolbox (5.8) sct_dmri_separate_b0_and_dwi -i museDTI.nii.gz -bvec bvecs.txt -- Input parameters: input file ............museDTI.nii.gz bvecs file ............bvecs.txt bvals file ............ average ...............1 Creating temporary folder (/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230205102118.047341-dmri_separate-jsptdam9) 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 bvecs.txt in /Users/2391266776qq.com/Downloads/CSM/data/museDTI (contents: ['DTI', 'museDTI.nii.gz', '.DS_Store', 'museDTI.json', 'museDTI.bvec', 'museDTI.bval']) 2391266776qq.com@ShydeMacBook-Pro museDTI % sct_dmri_separate_b0_and_dwi -i museDTI.nii.gz -bvec bvec.txt -- Spinal Cord Toolbox (5.8) sct_dmri_separate_b0_and_dwi -i museDTI.nii.gz -bvec bvec.txt -- Input parameters: input file ............museDTI.nii.gz bvecs file ............bvec.txt bvals file ............ average ...............1 Creating temporary folder (/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230205102245.232968-dmri_separate-1gtq526x) 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 bvec.txt in /Users/2391266776qq.com/Downloads/CSM/data/museDTI (contents: ['DTI', 'museDTI.nii.gz', '.DS_Store', 'museDTI.json', 'museDTI.bvec', 'museDTI.bval']) 2391266776qq.com@ShydeMacBook-Pro museDTI % ls DTI museDTI.bval museDTI.bvec museDTI.json museDTI.nii.gz 2391266776qq.com@ShydeMacBook-Pro museDTI % sct_dmri_separate_b0_and_dwi -i museDTI.nii.gz -bvec museDTIbvec.txt -- Spinal Cord Toolbox (5.8) sct_dmri_separate_b0_and_dwi -i museDTI.nii.gz -bvec museDTIbvec.txt -- Input parameters: input file ............museDTI.nii.gz bvecs file ............museDTIbvec.txt bvals file ............ average ...............1 Creating temporary folder (/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230205102353.362119-dmri_separate-9gma7w8x) 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 museDTIbvec.txt in /Users/2391266776qq.com/Downloads/CSM/data/museDTI (contents: ['DTI', 'museDTI.nii.gz', '.DS_Store', 'museDTI.json', 'museDTI.bvec', 'museDTI.bval']) 2391266776qq.com@ShydeMacBook-Pro museDTI % ls DTI museDTI.bval museDTI.bvec museDTI.json museDTI.nii.gz 2391266776qq.com@ShydeMacBook-Pro museDTI % sct_dmri_separate_b0_and_dwi -i museDTI.nii.gz -bvec museDTI.bvec.txt -- Spinal Cord Toolbox (5.8) sct_dmri_separate_b0_and_dwi -i museDTI.nii.gz -bvec museDTI.bvec.txt -- Input parameters: input file ............museDTI.nii.gz bvecs file ............museDTI.bvec.txt bvals file ............ average ...............1 Creating temporary folder (/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230205102915.803222-dmri_separate-3l37lghq) 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 museDTI.bvec.txt in /Users/2391266776qq.com/Downloads/CSM/data/museDTI (contents: ['DTI', 'museDTI.nii.gz', '.DS_Store', 'museDTI.json', 'museDTI.bvec', 'museDTI.bval']) 2391266776qq.com@ShydeMacBook-Pro museDTI % sct_dmri_separate_b0_and_dwi -i museDTI.nii.gz -bvec museDTI.bvec -- Spinal Cord Toolbox (5.8) sct_dmri_separate_b0_and_dwi -i museDTI.nii.gz -bvec museDTI.bvec -- Input parameters: input file ............museDTI.nii.gz bvecs file ............museDTI.bvec bvals file ............ average ...............1 Creating temporary folder (/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230205103006.626585-dmri_separate-idwpf_ll) Copy files into temporary folder... cp /Users/2391266776qq.com/Downloads/CSM/data/museDTI/museDTI.bvec /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230205103006.626585-dmri_separate-idwpf_ll/bvecs Get dimensions data... .. 256 x 256 x 23 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/data/museDTI/museDTI_b0.nii.gz File created: /Users/2391266776qq.com/Downloads/CSM/data/museDTI/museDTI_dwi.nii.gz File created: /Users/2391266776qq.com/Downloads/CSM/data/museDTI/museDTI_b0_mean.nii.gz File created: /Users/2391266776qq.com/Downloads/CSM/data/museDTI/museDTI_dwi_mean.nii.gz Remove temporary files... rm -rf /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230205103006.626585-dmri_separate-idwpf_ll Finished! Elapsed time: 2s 2391266776qq.com@ShydeMacBook-Pro museDTI % sct_deepseg_sc -i museDTI_dwi_mean.nii.gz -c dwi -qc ~/qc_CSM -- Spinal Cord Toolbox (5.8) sct_deepseg_sc -i museDTI_dwi_mean.nii.gz -c dwi -qc /Users/2391266776qq.com/qc_CSM -- 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-20230205103237.342269-hpbbex5y) Reorient the image to RPI, if necessary... Finding the spinal cord centerline... Creating temporary folder (/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230205103238.263790-covx7hbw) Remove temporary files... rm -rf /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230205103238.263790-covx7hbw 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%|################| 23/23 [00:00<00:00, 211.00iter/s] Remove temporary files... rm -rf /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230205103237.342269-hpbbex5y *** 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_CSM/CSM/data/museDTI/sct_deepseg_sc/2023_02_05_103241.439516/bkg_img.png cp /Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/reports/assets/_assets/css/bootstrap.min.css /Users/2391266776qq.com/qc_CSM/_assets/css cp /Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/reports/assets/_assets/css/bootstrap-table.min.css /Users/2391266776qq.com/qc_CSM/_assets/css cp /Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/reports/assets/_assets/css/select2.min.css /Users/2391266776qq.com/qc_CSM/_assets/css cp /Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/reports/assets/_assets/css/bootstrap.min.css.map /Users/2391266776qq.com/qc_CSM/_assets/css cp /Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/reports/assets/_assets/css/style.css /Users/2391266776qq.com/qc_CSM/_assets/css cp /Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/reports/assets/_assets/css/bootstrap-theme.min.css /Users/2391266776qq.com/qc_CSM/_assets/css cp /Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/reports/assets/_assets/js/select2.min.js /Users/2391266776qq.com/qc_CSM/_assets/js cp /Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/reports/assets/_assets/js/filesaver.min.js /Users/2391266776qq.com/qc_CSM/_assets/js cp /Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/reports/assets/_assets/js/jquery-3.1.0.min.js /Users/2391266776qq.com/qc_CSM/_assets/js cp /Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/reports/assets/_assets/js/bootstrap-table.min.js /Users/2391266776qq.com/qc_CSM/_assets/js cp /Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/reports/assets/_assets/js/main.js /Users/2391266776qq.com/qc_CSM/_assets/js cp /Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/reports/assets/_assets/js/bootstrap.min.js /Users/2391266776qq.com/qc_CSM/_assets/js cp /Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/reports/assets/_assets/js/animation.js /Users/2391266776qq.com/qc_CSM/_assets/js cp /Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/reports/assets/_assets/js/yaml.min.js /Users/2391266776qq.com/qc_CSM/_assets/js cp /Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/reports/assets/_assets/imgs/f-icon.png /Users/2391266776qq.com/qc_CSM/_assets/imgs cp /Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/reports/assets/_assets/imgs/axial.png /Users/2391266776qq.com/qc_CSM/_assets/imgs cp /Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/reports/assets/_assets/imgs/keyright.png /Users/2391266776qq.com/qc_CSM/_assets/imgs cp /Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/reports/assets/_assets/imgs/keydown.png /Users/2391266776qq.com/qc_CSM/_assets/imgs cp /Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/reports/assets/_assets/imgs/keyup.png /Users/2391266776qq.com/qc_CSM/_assets/imgs cp /Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/reports/assets/_assets/imgs/sagittal.png /Users/2391266776qq.com/qc_CSM/_assets/imgs cp /Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/reports/assets/_assets/imgs/sct_logo.png /Users/2391266776qq.com/qc_CSM/_assets/imgs cp /Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.woff /Users/2391266776qq.com/qc_CSM/_assets/fonts cp /Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.eot /Users/2391266776qq.com/qc_CSM/_assets/fonts cp /Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.woff2 /Users/2391266776qq.com/qc_CSM/_assets/fonts cp /Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.ttf /Users/2391266776qq.com/qc_CSM/_assets/fonts cp /Users/2391266776qq.com/sct_5.8/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.svg /Users/2391266776qq.com/qc_CSM/_assets/fonts Successfully generated the QC results in /Users/2391266776qq.com/qc_CSM/_json/qc_2023_02_05_103241.439516.json To see the results in a browser, type: open /Users/2391266776qq.com/qc_CSM/index.html Done! To view results, run one of the following commands (depending on your preferred viewer): fslview_deprecated /Users/2391266776qq.com/Downloads/CSM/data/museDTI/museDTI_dwi_mean.nii.gz -l Greyscale /Users/2391266776qq.com/Downloads/CSM/data/museDTI/museDTI_dwi_mean_seg.nii.gz -l Red -t 0.7 & fslview /Users/2391266776qq.com/Downloads/CSM/data/museDTI/museDTI_dwi_mean.nii.gz -l Greyscale /Users/2391266776qq.com/Downloads/CSM/data/museDTI/museDTI_dwi_mean_seg.nii.gz -l Red -t 0.7 & 2391266776qq.com@ShydeMacBook-Pro museDTI % sct_create_mask -i museDTI_dwi_mean.nii.gz -p centerline,museDTI_dwi_mean_seg.nii.gz -f cylinder -size 35mm -- Spinal Cord Toolbox (5.8) sct_create_mask -i museDTI_dwi_mean.nii.gz -p centerline,museDTI_dwi_mean_seg.nii.gz -f cylinder -size 35mm -- OK: museDTI_dwi_mean_seg.nii.gz Creating temporary folder (/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230205103417.274806-create_mask-8gy4bawo) Orientation: RPI Dimensions: (256, 256, 23, 1, 0.7813, 0.7813, 3.9999924, 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 '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-20230205103417.274806-create_mask-8gy4bawo Done! To view results, run one of the following commands (depending on your preferred viewer): fslview_deprecated /Users/2391266776qq.com/Downloads/CSM/data/museDTI/museDTI_dwi_mean.nii.gz -l Greyscale /Users/2391266776qq.com/Downloads/CSM/data/museDTI/mask_museDTI_dwi_mean.nii.gz -l Red -t 0.5 & fslview /Users/2391266776qq.com/Downloads/CSM/data/museDTI/museDTI_dwi_mean.nii.gz -l Greyscale /Users/2391266776qq.com/Downloads/CSM/data/museDTI/mask_museDTI_dwi_mean.nii.gz -l Red -t 0.5 & 2391266776qq.com@ShydeMacBook-Pro museDTI % sct_dmri_moco -i museDTI.nii.gz -m mask_museDTI_dwi_mean.nii.gz -bvec museDTI.bvec \ -qc ~/qc_CSM -qc-seg museDTI_dwi_mean_seg.nii.gz -- Spinal Cord Toolbox (5.8) sct_dmri_moco -i museDTI.nii.gz -m mask_museDTI_dwi_mean.nii.gz -bvec museDTI.bvec -qc /Users/2391266776qq.com/qc_CSM -qc-seg museDTI_dwi_mean_seg.nii.gz -- Input parameters: Input file ............ museDTI.nii.gz Group size ............ 3 Creating temporary folder (/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230205103737.571225-moco-_e_pjkae) Copying input data to tmp folder and convert to nii... Get dimensions of data... 256 x 256 x 23 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_CSM/CSM/data/museDTI/sct_dmri_moco/2023_02_05_104009.738440/overlay_img.gif Animation.save using Successfully generated the QC results in /Users/2391266776qq.com/qc_CSM/_json/qc_2023_02_05_104009.738440.json To see the results in a browser, type: open /Users/2391266776qq.com/qc_CSM/index.html Done! To view results, run one of the following commands (depending on your preferred viewer): fslview_deprecated -m ortho,ortho museDTI_moco.nii.gz museDTI.nii.gz & fslview -m ortho,ortho museDTI_moco.nii.gz museDTI.nii.gz & 2391266776qq.com@ShydeMacBook-Pro museDTI % sct_deepseg_sc -i museDTI_moco_dwi_mean.nii.gz -c dwi -qc ~/qc_CSM -- Spinal Cord Toolbox (5.8) sct_deepseg_sc -i museDTI_moco_dwi_mean.nii.gz -c dwi -qc /Users/2391266776qq.com/qc_CSM -- 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-20230205104109.281576-2t4nmmiy) Reorient the image to RPI, if necessary... Finding the spinal cord centerline... Creating temporary folder (/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230205104110.410942-0ji2ut88) Remove temporary files... rm -rf /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230205104110.410942-0ji2ut88 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%|################| 23/23 [00:00<00:00, 251.24iter/s] Remove temporary files... rm -rf /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230205104109.281576-2t4nmmiy *** 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_CSM/CSM/data/museDTI/sct_deepseg_sc/2023_02_05_104113.663818/bkg_img.png Successfully generated the QC results in /Users/2391266776qq.com/qc_CSM/_json/qc_2023_02_05_104113.663818.json To see the results in a browser, type: open /Users/2391266776qq.com/qc_CSM/index.html Done! To view results, run one of the following commands (depending on your preferred viewer): fslview_deprecated /Users/2391266776qq.com/Downloads/CSM/data/museDTI/museDTI_moco_dwi_mean.nii.gz -l Greyscale /Users/2391266776qq.com/Downloads/CSM/data/museDTI/museDTI_moco_dwi_mean_seg.nii.gz -l Red -t 0.7 & fslview /Users/2391266776qq.com/Downloads/CSM/data/museDTI/museDTI_moco_dwi_mean.nii.gz -l Greyscale /Users/2391266776qq.com/Downloads/CSM/data/museDTI/museDTI_moco_dwi_mean_seg.nii.gz -l Red -t 0.7 & 2391266776qq.com@ShydeMacBook-Pro museDTI % sct_register_multimodal -i "${SCT_DIR}/data/PAM50/template/PAM50_t1.nii.gz" \ -iseg "${SCT_DIR}/data/PAM50/template/PAM50_cord.nii.gz" \ -d museDTI_moco_dwi_mean.nii.gz \ -dseg museDTI_moco_dwi_mean_seg.nii.gz \ -initwarp ../t2s/warp_template2t2s.nii.gz \ -initwarpinv ../t2s/warp_t2s2template.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_CSM -- 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 museDTI_moco_dwi_mean.nii.gz -dseg museDTI_moco_dwi_mean_seg.nii.gz -initwarp ../t2s/warp_template2t2s.nii.gz -initwarpinv ../t2s/warp_t2s2template.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_CSM -- Input parameters: Source .............. /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_t1.nii.gz (141, 141, 991) Destination ......... museDTI_moco_dwi_mean.nii.gz (256, 256, 23) Init transfo ........ /Users/2391266776qq.com/Downloads/CSM/data/t2s/warp_template2t2s.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-20230205104559.422804-register-1_poco_h) Copying input data to tmp folder and convert to nii... Skip step=0 and replace with initial transformations: /Users/2391266776qq.com/Downloads/CSM/data/t2s/warp_template2t2s.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/data/t2s/warp_template2t2s.nii.gz -r dest_seg_RPI.nii -n NearestNeighbor # in /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230205104559.422804-register-1_poco_h 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-20230205104601.245992-register-wzt7l_eb) Copy input data to temp folder... Get image dimensions of destination image... matrix size: 256 x 256 x 23 voxel size: 0.7813mm x 0.7813mm x 23mm Split input segmentation... Split destination segmentation... Estimate cord angle for each slice: 0%| | 0/23 [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-20230205104559.422804-register-1_poco_h cp step1InverseWarp.nii.gz /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230205104559.422804-register-1_poco_h rm -rf /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230205104601.245992-register-wzt7l_eb -- 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/data/t2s/warp_template2t2s.nii.gz -r dest_seg_RPI.nii -n NearestNeighbor # in /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230205104559.422804-register-1_poco_h 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-20230205104607.593609-register-bob99ejb) Copy input data to temp folder... Get image dimensions of destination image... matrix size: 256 x 256 x 23 voxel size: 0.7813mm x 0.7813mm x 23mm Split input volume... Split destination volume... Registering slice 0/22... /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-20230205104607.593609-register-bob99ejb Registering slice 1/22... /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-20230205104607.593609-register-bob99ejb Registering slice 2/22... /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-20230205104607.593609-register-bob99ejb Registering slice 3/22... /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-20230205104607.593609-register-bob99ejb Registering slice 4/22... /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-20230205104607.593609-register-bob99ejb Registering slice 5/22... /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-20230205104607.593609-register-bob99ejb Registering slice 6/22... /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-20230205104607.593609-register-bob99ejb Registering slice 7/22... /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-20230205104607.593609-register-bob99ejb Registering slice 8/22... /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-20230205104607.593609-register-bob99ejb Registering slice 9/22... /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-20230205104607.593609-register-bob99ejb Registering slice 10/22... /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-20230205104607.593609-register-bob99ejb Registering slice 11/22... /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-20230205104607.593609-register-bob99ejb Registering slice 12/22... /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-20230205104607.593609-register-bob99ejb Registering slice 13/22... /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-20230205104607.593609-register-bob99ejb Registering slice 14/22... /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-20230205104607.593609-register-bob99ejb Registering slice 15/22... /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-20230205104607.593609-register-bob99ejb Registering slice 16/22... /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-20230205104607.593609-register-bob99ejb Registering slice 17/22... /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-20230205104607.593609-register-bob99ejb Registering slice 18/22... /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-20230205104607.593609-register-bob99ejb Registering slice 19/22... /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-20230205104607.593609-register-bob99ejb Registering slice 20/22... /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-20230205104607.593609-register-bob99ejb Registering slice 21/22... /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-20230205104607.593609-register-bob99ejb Registering slice 22/22... /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-20230205104607.593609-register-bob99ejb Merge warping fields along z... Move warping fields... cp step2Warp.nii.gz /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230205104559.422804-register-1_poco_h cp step2InverseWarp.nii.gz /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230205104559.422804-register-1_poco_h rm -rf /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230205104607.593609-register-bob99ejb 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/data/t2s/warp_template2t2s.nii.gz # in /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230205104559.422804-register-1_poco_h /Users/2391266776qq.com/sct_5.8/bin/isct_ComposeMultiTransform 3 warp_dest2src.nii.gz -R src.nii /Users/2391266776qq.com/Downloads/CSM/data/t2s/warp_t2s2template.nii.gz warp_inverse_1.nii.gz warp_inverse_2.nii.gz # in /private/var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230205104559.422804-register-1_poco_h 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-20230205104559.422804-register-1_poco_h 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-20230205104559.422804-register-1_poco_h Generate output files... File created: PAM50_t1_reg.nii.gz mv /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230205104559.422804-register-1_poco_h/warp_src2dest.nii.gz warp_template2dmri.nii.gz File created: warp_template2dmri.nii.gz File created: museDTI_moco_dwi_mean_reg.nii.gz mv /var/folders/w9/_8cxczg96s9ct_6gjrjdfnv40000gn/T/sct-20230205104559.422804-register-1_poco_h/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-20230205104559.422804-register-1_poco_h Finished! Elapsed time: 34s *** 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/sct_5.8/spinalcordtoolbox/reports/qc.py:398: RuntimeWarning: invalid value encountered in divide b = (np.float32(img) - min_) / (max_ - min_) /Users/2391266776qq.com/qc_CSM/CSM/data/museDTI/sct_register_multimodal/2023_02_05_104634.671785/bkg_img.png Successfully generated the QC results in /Users/2391266776qq.com/qc_CSM/_json/qc_2023_02_05_104634.671785.json To see the results in a browser, type: open /Users/2391266776qq.com/qc_CSM/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 museDTI_moco_dwi_mean_reg.nii.gz & fslview /Users/2391266776qq.com/sct_5.8/data/PAM50/template/PAM50_t1.nii.gz museDTI_moco_dwi_mean_reg.nii.gz & Done! To view results, run one of the following commands (depending on your preferred viewer): fslview_deprecated museDTI_moco_dwi_mean.nii.gz PAM50_t1_reg.nii.gz & fslview museDTI_moco_dwi_mean.nii.gz PAM50_t1_reg.nii.gz & 2391266776qq.com@ShydeMacBook-Pro museDTI % sct_warp_template -d museDTI_moco_dwi_mean.nii.gz -w warp_template2dmri.nii.gz -qc ~/qc_CSM -- Spinal Cord Toolbox (5.8) sct_warp_template -d museDTI_moco_dwi_mean.nii.gz -w warp_template2dmri.nii.gz -qc /Users/2391266776qq.com/qc_CSM -- Check parameters: Working directory ........ /Users/2391266776qq.com/Downloads/CSM/data/museDTI Destination image ........ museDTI_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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n NearestNeighbor # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n NearestNeighbor # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n NearestNeighbor # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n NearestNeighbor # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI 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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI /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 museDTI_moco_dwi_mean.nii.gz -n Linear # in /Users/2391266776qq.com/Downloads/CSM/data/museDTI 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 Image header specifies datatype 'float64', 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/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_CSM/CSM/data/museDTI/sct_warp_template/2023_02_05_104849.871305/bkg_img.png Successfully generated the QC results in /Users/2391266776qq.com/qc_CSM/_json/qc_2023_02_05_104849.871305.json To see the results in a browser, type: open /Users/2391266776qq.com/qc_CSM/index.html Done! To view results, run one of the following commands (depending on your preferred viewer): fslview_deprecated museDTI_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 museDTI_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 museDTI % sct_dmri_compute_dti -i museDTI_moco.nii.gz -bval museDTI.bval -bvec museDTI.bvec -- Spinal Cord Toolbox (5.8) sct_dmri_compute_dti -i museDTI_moco.nii.gz -bval museDTI.bval -bvec museDTI.bvec -- data.shape (256, 256, 23, 13) Computing tensor using "standard" method... Computing metrics... 2391266776qq.com@ShydeMacBook-Pro museDTI % sct_extract_metric -i dti_FA.nii.gz -f label/atlas \ -l 51 -method map \ -vert 2:7 -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 2:7 -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 museDTI % sct_extract_metric -i dti_AD.nii.gz -f label/atlas \ -l 51 -method map \ -vert 2:7 -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 2:7 -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 museDTI % sct_extract_metric -i dti_AD.nii.gz -f label/atlas \ -l 51 -method map \ -vert 2:3 -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 2:3 -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 museDTI % sct_extract_metric -i dti_AD.nii.gz -f label/atlas \ -l 51 -method map \ -vert 2:3 -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 2:3 -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 museDTI % sct_check_dependencies -- Spinal Cord Toolbox (5.8) sct_check_dependencies -- SYSTEM INFORMATION ------------------ SCT info: - version: 5.8 - path: /Users/2391266776qq.com/sct_5.8 OS: osx (macOS-10.16-x86_64-i386-64bit) CPU cores: Available: 8, Used by ITK functions: 8 RAM: Total: 16384MB, Used: 1749MB, Available: 1309MB OPTIONAL DEPENDENCIES --------------------- Check FSLeyes version...............................[ ] (127, '/bin/sh: fsleyes: command not found') MANDATORY DEPENDENCIES ---------------------- Check Python executable.............................[OK] Using bundled python 3.8.16 (default, Jan 17 2023, 16:42:09) [Clang 14.0.6 ] at /Users/2391266776qq.com/sct_5.8/python/envs/venv_sct/bin/python Check if data are installed.........................[OK] Check if dipy is installed..........................[OK] (1.5.0) Check if ivadomed is installed......................[OK] (2.9.7) Check if matplotlib is installed....................[OK] (3.6.2) Check if nibabel is installed.......................[OK] (3.2.2) Check if nilearn is installed.......................[OK] (0.9.2) Check if numpy is installed.........................[OK] (1.23.5) Check if onnxruntime is installed...................[OK] (1.13.1) Check if pandas is installed........................[OK] (1.4.4) Check if portalocker is installed...................[OK] (2.6.0) Check if psutil is installed........................[OK] (5.9.4) Check if pyqt5 is installed.........................[OK] (5.14.2) Check if pytest is installed........................[OK] (7.2.0) Check if pytest-cov is installed....................[OK] (4.0.0) Check if raven is installed.........................[OK] Check if requests is installed......................[OK] (2.28.1) Check if requirements-parser is installed...........[OK] Check if scipy is installed.........................[OK] (1.9.3) Check if scikit-image is installed..................[OK] (0.19.3) Check if scikit-learn is installed..................[OK] (1.1.3) Check if xlwt is installed..........................[OK] (1.3.0) Check if tqdm is installed..........................[OK] (4.64.1) Check if transforms3d is installed..................[OK] (0.4.1) Check if urllib3 is installed.......................[OK] (1.26.13) Check if pytest_console_scripts is installed........[OK] Check if pyyaml is installed........................[OK] (6.0) Check if voxelmorph is installed....................[OK] (0.2) Check if wquantiles is installed....................[OK] (0.4) Check if spinalcordtoolbox is installed.............[OK] Check ANTs compatibility with OS ...................[OK] Check PropSeg compatibility with OS ................[OK] Check if figure can be opened with PyQt.............[OK] Check if figure can be opened with matplotlib.......[OK] (Using GUI backend: 'QtAgg') 2391266776qq.com@ShydeMacBook-Pro museDTI %