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  1. [jcohen@gra-login3 log]$ cat process_data_sub-unf06.log
  2. + set -e
  3. + trap 'echo Caught Keyboard Interrupt within script. Exiting now.; exit' INT
  4. ++ date +%s
  5. + start=1598284474
  6. + SUBJECT=sub-unf06
  7. + config_script=/home/jcohen/csa-atrophy/config_script_t1.yml
  8. + echo 'SUBJECT: sub-unf06'
  9. SUBJECT: sub-unf06
  10. + echo 'config_script: /home/jcohen/csa-atrophy/config_script_t1.yml'
  11. config_script: /home/jcohen/csa-atrophy/config_script_t1.yml
  12. ++ yaml_parser -o n_transfo -i /home/jcohen/csa-atrophy/config_script_t1.yml
  13. + n_transfo=3
  14. ++ yaml_parser -o rescaling -i /home/jcohen/csa-atrophy/config_script_t1.yml
  15. + rescaling='[1, 0.99]'
  16. ++ tr ''\''' ' '
  17. ++ tr , ' '
  18. ++ tr '[]' ' '
  19. ++ echo '[1,' '0.99]'
  20. + R_COEFS=' 1 0.99 '
  21. ++ yaml_parser -o contrast -i /home/jcohen/csa-atrophy/config_script_t1.yml
  22. + contrast=t1
  23. ++ yaml_parser -o transfo_file -i /home/jcohen/csa-atrophy/config_script_t1.yml
  24. + transfo_file=transfo_values.csv
  25. + echo 'transfo_file: transfo_values.csv'
  26. transfo_file: transfo_values.csv
  27. + sct_check_dependencies -short
  28.  
  29. --
  30. Spinal Cord Toolbox (git-master-253936cfc07712c587d9f4cfbbcb760f151172f0)
  31.  
  32. SCT info:
  33. - version: git-master-253936cfc07712c587d9f4cfbbcb760f151172f0
  34. - path: /home/jcohen/sct
  35. OS: linux (Linux-3.10.0-1127.8.2.el7.x86_64-x86_64-with-centos-7.8.2003-Core)
  36. CPU cores: Available: 32, Used by SCT: 1
  37. RAM: MemTotal: 527986272 kB
  38. total used free shared buff/cache available
  39. Mem: 515611 121291 342871 3724 51448 384671
  40. Swap: 10239 648 9591
  41. + cd /scratch/jcohen/results_csa_t1_20200824/data_processed
  42. + cp -r /home/jcohen/data-multi-subject/sub-unf06 .
  43. + cd sub-unf06
  44. + rm -r dwi
  45. + cd anat
  46. + '[' t1 == t2 ']'
  47. + '[' t1 == t1 ']'
  48. + contrast_str=T1w
  49. + interp=1x1x1
  50. + file=sub-unf06_T1w
  51. + sct_image -i sub-unf06_T1w.nii.gz -setorient RPI -o sub-unf06_T1w_RPI.nii.gz
  52.  
  53. --
  54. Spinal Cord Toolbox (git-master-253936cfc07712c587d9f4cfbbcb760f151172f0)
  55.  
  56. sub-unf06_T1w.nii.gz
  57. Generate output files...
  58. + file=sub-unf06_T1w_RPI
  59. + sct_resample -i sub-unf06_T1w_RPI.nii.gz -mm 1x1x1 -o sub-unf06_T1w_RPI_r.nii.gz
  60.  
  61. --
  62. Spinal Cord Toolbox (git-master-253936cfc07712c587d9f4cfbbcb760f151172f0)
  63.  
  64. load data...
  65. + file=sub-unf06_T1w_RPI_r
  66. ++ date +%s
  67. + end=1598284491
  68. + runtime=17
  69. + echo '+++++++++++ TIME: Duration of reorienting and resampling: 0hrs 0min 17sec'
  70. +++++++++++ TIME: Duration of reorienting and resampling: 0hrs 0min 17sec
  71. ++ date +%s
  72. + start=1598284491
  73. + segment_if_does_not_exist sub-unf06_T1w_RPI_r t1 '-qc /scratch/jcohen/results_csa_t1_20200824/qc -qc-subject sub-unf06'
  74. + local file=sub-unf06_T1w_RPI_r
  75. + local contrast=t1
  76. + local 'qc=-qc /scratch/jcohen/results_csa_t1_20200824/qc -qc-subject sub-unf06'
  77. + FILESEG=sub-unf06_T1w_RPI_r_seg
  78. + FILESEGMANUAL=/home/jcohen/data-multi-subject/derivatives/labels/sub-unf06/anat/sub-unf06_T1w_RPI_r_seg-manual.nii.gz
  79. + '[' -e /home/jcohen/data-multi-subject/derivatives/labels/sub-unf06/anat/sub-unf06_T1w_RPI_r_seg-manual.nii.gz ']'
  80. + sct_deepseg_sc -i sub-unf06_T1w_RPI_r.nii.gz -c t1 -qc /scratch/jcohen/results_csa_t1_20200824/qc -qc-subject sub-unf06
  81.  
  82. --
  83. Spinal Cord Toolbox (git-master-253936cfc07712c587d9f4cfbbcb760f151172f0)
  84.  
  85. Config deepseg_sc:
  86. Centerline algorithm: svm
  87. Brain in image: True
  88. Kernel dimension: 2d
  89. Contrast: t1
  90. Threshold: 0.15
  91.  
  92. Create temporary folder (/tmp/sct-20200824115459.539535-20gl8n_6)...
  93. Reorient the image to RPI, if necessary...
  94. Finding the spinal cord centerline...
  95. Remove temporary files...
  96. rm -rf /tmp/sct-20200824115553.976076-p3w6ect4
  97. Cropping the image around the spinal cord...
  98. Normalizing the intensity...
  99. Segmenting the spinal cord using deep learning on 2D patches...
  100. Reassembling the image...
  101. Resampling the segmentation to the native image resolution using linear interpolation...
  102. Binarizing the resampled segmentation...
  103. Removing small objects above slice #173
  104. Remove temporary files...
  105. rm -rf /tmp/sct-20200824115459.539535-20gl8n_6
  106.  
  107. *** Generate Quality Control (QC) html report ***
  108. Resample images to 0.6x0.6 mm
  109. QcImage: layout with Axial slice
  110. Compute center of mass at each slice
  111. cp /home/jcohen/sct/spinalcordtoolbox/reports/assets/_assets/css/select2.min.css /scratch/jcohen/results_csa_t1_20200824/qc/_assets/css
  112. cp /home/jcohen/sct/spinalcordtoolbox/reports/assets/_assets/css/style.css /scratch/jcohen/results_csa_t1_20200824/qc/_assets/css
  113. cp /home/jcohen/sct/spinalcordtoolbox/reports/assets/_assets/css/bootstrap.min.css.map /scratch/jcohen/results_csa_t1_20200824/qc/_assets/css
  114. cp /home/jcohen/sct/spinalcordtoolbox/reports/assets/_assets/css/bootstrap-table.min.css /scratch/jcohen/results_csa_t1_20200824/qc/_assets/css
  115. cp /home/jcohen/sct/spinalcordtoolbox/reports/assets/_assets/css/bootstrap.min.css /scratch/jcohen/results_csa_t1_20200824/qc/_assets/css
  116. cp /home/jcohen/sct/spinalcordtoolbox/reports/assets/_assets/css/bootstrap-theme.min.css /scratch/jcohen/results_csa_t1_20200824/qc/_assets/css
  117. cp /home/jcohen/sct/spinalcordtoolbox/reports/assets/_assets/js/bootstrap.min.js /scratch/jcohen/results_csa_t1_20200824/qc/_assets/js
  118. cp /home/jcohen/sct/spinalcordtoolbox/reports/assets/_assets/js/bootstrap-table.min.js /scratch/jcohen/results_csa_t1_20200824/qc/_assets/js
  119. cp /home/jcohen/sct/spinalcordtoolbox/reports/assets/_assets/js/animation.js /scratch/jcohen/results_csa_t1_20200824/qc/_assets/js
  120. cp /home/jcohen/sct/spinalcordtoolbox/reports/assets/_assets/js/select2.min.js /scratch/jcohen/results_csa_t1_20200824/qc/_assets/js
  121. cp /home/jcohen/sct/spinalcordtoolbox/reports/assets/_assets/js/jquery-3.1.0.min.js /scratch/jcohen/results_csa_t1_20200824/qc/_assets/js
  122. cp /home/jcohen/sct/spinalcordtoolbox/reports/assets/_assets/js/main.js /scratch/jcohen/results_csa_t1_20200824/qc/_assets/js
  123. cp /home/jcohen/sct/spinalcordtoolbox/reports/assets/_assets/imgs/sagittal.png /scratch/jcohen/results_csa_t1_20200824/qc/_assets/imgs
  124. cp /home/jcohen/sct/spinalcordtoolbox/reports/assets/_assets/imgs/axial.png /scratch/jcohen/results_csa_t1_20200824/qc/_assets/imgs
  125. cp /home/jcohen/sct/spinalcordtoolbox/reports/assets/_assets/imgs/sct_logo.png /scratch/jcohen/results_csa_t1_20200824/qc/_assets/imgs
  126. cp /home/jcohen/sct/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.woff /scratch/jcohen/results_csa_t1_20200824/qc/_assets/fonts
  127. cp /home/jcohen/sct/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.eot /scratch/jcohen/results_csa_t1_20200824/qc/_assets/fonts
  128. cp /home/jcohen/sct/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.ttf /scratch/jcohen/results_csa_t1_20200824/qc/_assets/fonts
  129. cp /home/jcohen/sct/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.svg /scratch/jcohen/results_csa_t1_20200824/qc/_assets/fonts
  130. cp /home/jcohen/sct/spinalcordtoolbox/reports/assets/_assets/fonts/glyphicons-halflings-regular.woff2 /scratch/jcohen/results_csa_t1_20200824/qc/_assets/fonts
  131. Successfully generated the QC results in /scratch/jcohen/results_csa_t1_20200824/qc/_json/qc_2020_08_24_115702.422701.json
  132. Use the following command to see the results in a browser:
  133. xdg-open "/scratch/jcohen/results_csa_t1_20200824/qc/index.html"
  134. + file_seg=sub-unf06_T1w_RPI_r_seg
  135. ++ date +%s
  136. + end=1598284624
  137. + runtime=133
  138. + echo '+++++++++++ TIME: Duration of segmentation on non cropped image: 0hrs 2min 13sec'
  139. +++++++++++ TIME: Duration of segmentation on non cropped image: 0hrs 2min 13sec
  140. ++ date +%s
  141. + start=1598284624
  142. + label_if_does_not_exist sub-unf06_T1w_RPI_r sub-unf06_T1w_RPI_r_seg t1 T1w
  143. + local file=sub-unf06_T1w_RPI_r
  144. + local file_seg=sub-unf06_T1w_RPI_r_seg
  145. + local contrast=t1
  146. + local contrast_str=T1w
  147. + FILELABEL=sub-unf06_T1w_RPI_r_labels
  148. + FILELABELMANUAL=/home/jcohen/data-multi-subject/derivatives/labels/sub-unf06/anat/sub-unf06_T1w_RPI_r_labels-manual.nii.gz
  149. + '[' -e /home/jcohen/data-multi-subject/derivatives/labels/sub-unf06/anat/sub-unf06_T1w_RPI_r_labels-manual.nii.gz ']'
  150. + sct_label_vertebrae -i sub-unf06_T1w_RPI_r.nii.gz -s sub-unf06_T1w_RPI_r_seg.nii.gz -c t1 -qc /scratch/jcohen/results_csa_t1_20200824/qc -qc-subject sub-unf06
  151.  
  152. --
  153. Spinal Cord Toolbox (git-master-253936cfc07712c587d9f4cfbbcb760f151172f0)
  154.  
  155. Folder /scratch/jcohen/results_csa_t1_20200824/qc has been created.
  156.  
  157. Create temporary folder (/tmp/sct-20200824115706.061159-label_vertebrae-mv5jvq63)...
  158.  
  159. Copying input data to tmp folder...
  160.  
  161. Straighten spinal cord...
  162.  
  163. Create temporary folder (/tmp/sct-20200824115707.278393-straighten_spinalcord-hlns7gei)...
  164.  
  165. Copy files to tmp folder...
  166. Window length needs to be >= 3. Returning input signal.
  167. Window length needs to be >= 3. Returning input signal.
  168. Fitting centerline using B-spline approximation
  169. Error on approximation = 1.04 mm
  170. Error on approximation = 0.21 mm
  171. Error on approximation = 0.05 mm
  172. Error on approximation = 0.03 mm
  173. Error on approximation = 0.02 mm
  174. Error on approximation = 0.02 mm
  175. Error on approximation = 0.02 mm
  176. Create the straight space and the safe zone
  177. Length of spinal cord: 178.0595712416701
  178. Size of spinal cord in z direction: 173.0
  179. Ratio length/size: 1.0292460765414457
  180. Safe zone boundaries (curved space): [-83.09638977050781, 89.90361022949219]
  181. Safe zone boundaries (straight space): [-85.62617539134287, 92.43339585032724]
  182. Pad input volume to account for spinal cord length...
  183. Time to generate centerline: 27.0 ms
  184. Warping field generated: tmp.curve2straight.nii.gz
  185. Warping field generated: tmp.straight2curve.nii.gz
  186. Apply transformation to input image...
  187. /home/jcohen/sct/bin/isct_antsApplyTransforms -d 3 -r tmp.centerline_pad_crop.nii.gz -i data.nii -o tmp.anat_rigid_warp.nii.gz -t tmp.curve2straight.nii.gz -n 'BSpline[3]' # in /tmp/sct-20200824115707.278393-straighten_spinalcord-hlns7gei
  188. Generate output files...
  189. File created: ./warp_curve2straight.nii.gz
  190. File created: ./warp_straight2curve.nii.gz
  191. cp /tmp/sct-20200824115707.278393-straighten_spinalcord-hlns7gei/tmp.anat_rigid_warp.nii.gz ./straight_ref.nii.gz
  192. File created: ./data_straight.nii
  193. Remove temporary files...
  194. rm -rf /tmp/sct-20200824115707.278393-straighten_spinalcord-hlns7gei
  195.  
  196. Finished! Elapsed time: 108 s
  197.  
  198. Resample to 0.5mm isotropic...
  199. sct_resample -i data_straight.nii -mm 0.5x0.5x0.5 -x linear -o data_straightr.nii # in /tmp/sct-20200824115706.061159-label_vertebrae-mv5jvq63
  200.  
  201. Apply straightening to segmentation...
  202. /home/jcohen/sct/bin/isct_antsApplyTransforms -d 3 -i segmentation.nii -r data_straightr.nii -t warp_curve2straight.nii.gz -o segmentation_straight.nii -n Linear # in /tmp/sct-20200824115706.061159-label_vertebrae-mv5jvq63
  203. sct_maths -i segmentation_straight.nii -thr 0.5 -o segmentation_straight.nii # in /tmp/sct-20200824115706.061159-label_vertebrae-mv5jvq63
  204.  
  205. Create label to identify disc...
  206. Creating temporary folder...
  207. Run C2-C3 detector...
  208. C2-C3 detected...
  209. Remove temporary files...
  210. rm -rf /tmp/sct-20200824115902.632439-usilw9k0
  211. File /tmp/sct-20200824115706.061159-label_vertebrae-mv5jvq63/labelz.nii.gz already exists. Will overwrite it.
  212.  
  213. And apply straightening to label...
  214. /home/jcohen/sct/bin/isct_antsApplyTransforms -d 3 -i labelz.nii.gz -r data_straightr.nii -t warp_curve2straight.nii.gz -o labelz_straight.nii.gz -n NearestNeighbor # in /tmp/sct-20200824115706.061159-label_vertebrae-mv5jvq63
  215.  
  216. Get z and disc values from straight label...
  217. .. [280, 3]
  218.  
  219. Look for template...
  220. Path template: /home/jcohen/sct/data/PAM50
  221.  
  222. Open template and vertebral levels...
  223.  
  224. Disc values from template: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19]
  225. Z-values for each disc: [962, 939, 908, 871, 834, 801, 770, 736, 693, 647, 601, 552, 501, 450, 397, 343, 290, 232, 169, 106, 56]
  226. Distances between discs (in voxel): [23.0, 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, 63.0, 50.0]
  227.  
  228. Detect intervertebral discs...
  229. Current disc: 2 (z=280). Direction: superior
  230. .. Peak found: z=-5 (correlation = 0.6735053968732413)
  231. Current disc: 1 (z=306). Direction: superior
  232. .. correcting factor: 1.0
  233. .. Switching to inferior direction.
  234. Current disc: 3 (z=243). Direction: inferior
  235. .. Peak found: z=-2 (correlation = 0.728995560334394)
  236. .. correcting factor: 0.9594594594594594
  237. Current disc: 4 (z=205). Direction: inferior
  238. .. Peak found: z=3 (correlation = 0.7388355091912501)
  239. .. correcting factor: 0.9369369369369368
  240. Current disc: 5 (z=177). Direction: inferior
  241. .. Peak found: z=2 (correlation = 0.6333839261126878)
  242. .. correcting factor: 0.9223996723996724
  243. Current disc: 6 (z=150). Direction: inferior
  244. .. Peak found: z=1 (correlation = 0.6923391347451896)
  245. .. correcting factor: 0.9185648992100605
  246. Current disc: 7 (z=120). Direction: inferior
  247. .. Peak found: z=0 (correlation = 0.6291191491294454)
  248. .. correcting factor: 0.9174315336554426
  249. Current disc: 8 (z=81). Direction: inferior
  250. .. Peak found: z=-2 (correlation = 0.6910021673913839)
  251. .. correcting factor: 0.922582510575097
  252. Current disc: 9 (z=37). Direction: inferior
  253. .. Peak found: z=3 (correlation = 0.6909278407497623)
  254. .. correcting factor: 0.913237957622775
  255. Adding top disc based on adjusted template distance: #0
  256. .. approximate distance: 21
  257.  
  258. Un-straighten labeling...
  259. /home/jcohen/sct/bin/isct_antsApplyTransforms -d 3 -i segmentation_straight_labeled.nii -r segmentation.nii -t warp_straight2curve.nii.gz -o segmentation_labeled.nii -n NearestNeighbor # in /tmp/sct-20200824115706.061159-label_vertebrae-mv5jvq63
  260.  
  261. Clean labeled segmentation (correct interpolation errors)...
  262. File /tmp/sct-20200824115706.061159-label_vertebrae-mv5jvq63/segmentation_labeled.nii already exists. Will overwrite it.
  263.  
  264. Label discs...
  265.  
  266. Generate output files...
  267. File created: ./sub-unf06_T1w_RPI_r_seg_labeled.nii.gz
  268. File created: ./sub-unf06_T1w_RPI_r_seg_labeled_discs.nii.gz
  269. File created: ./warp_curve2straight.nii.gz
  270. File created: ./warp_straight2curve.nii.gz
  271. File created: ./straight_ref.nii.gz
  272.  
  273. Remove temporary files...
  274. rm -rf /tmp/sct-20200824115706.061159-label_vertebrae-mv5jvq63
  275.  
  276. *** Generate Quality Control (QC) html report ***
  277. Resample images to NonexNone mm
  278. QcImage: layout with Sagittal slice
  279. Successfully generated the QC results in /scratch/jcohen/results_csa_t1_20200824/qc/_json/qc_2020_08_24_115921.902717.json
  280. Use the following command to see the results in a browser:
  281. xdg-open "/scratch/jcohen/results_csa_t1_20200824/qc/index.html"
  282. + sct_label_utils -i sub-unf06_T1w_RPI_r_seg_labeled.nii.gz -vert-body 0 -o sub-unf06_T1w_RPI_r_labels.nii.gz
  283.  
  284. --
  285. Spinal Cord Toolbox (git-master-253936cfc07712c587d9f4cfbbcb760f151172f0)
  286.  
  287. Value = 1.0 : (94.3094958968347, 106.6271981242673, 153.6822977725674) --> ( 94.0, 107.0, 154.0)
  288. Value = 2.0 : (94.8192883895131, 104.7312734082397, 140.0365168539326) --> ( 95.0, 105.0, 140.0)
  289. Value = 3.0 : (95.28728813559322, 102.73813559322033, 124.35254237288136) --> ( 95.0, 103.0, 124.0)
  290. Value = 4.0 : (95.47850770478507, 100.41200324412003, 108.23276561232765) --> ( 95.0, 100.0, 108.0)
  291. Value = 5.0 : (95.39362699156514, 97.70759137769447, 93.28209934395501) --> ( 95.0, 98.0, 93.0)
  292. Value = 6.0 : (95.1880341880342, 94.63995726495726, 79.68482905982906) --> ( 95.0, 95.0, 80.0)
  293. Value = 7.0 : (94.88470873786407, 90.99514563106796, 65.53398058252426) --> ( 95.0, 91.0, 66.0)
  294. Value = 8.0 : (94.21221864951768, 86.19078242229368, 48.11146838156485) --> ( 94.0, 86.0, 48.0)
  295. Value = 9.0 : (93.49939831528279, 80.67509025270758, 28.557160048134776) --> ( 93.0, 81.0, 29.0)
  296. Value = 10.0 : (92.71603427172583, 74.81272949816402, 9.458996328029375) --> ( 93.0, 75.0, 9.0)
  297. + file_label=sub-unf06_T1w_RPI_r_seg_labeled
  298. ++ date +%s
  299. + end=1598284765
  300. + runtime=141
  301. + echo '+++++++++++ TIME: Duration of labelling: 0hrs 2min 21sec'
  302. +++++++++++ TIME: Duration of labelling: 0hrs 2min 21sec
  303. + sct_maths -i sub-unf06_T1w_RPI_r_seg.nii.gz -dilate 15 -shape cube -o sub-unf06_T1w_RPI_r_seg_dil.nii.gz
  304.  
  305. --
  306. Spinal Cord Toolbox (git-master-253936cfc07712c587d9f4cfbbcb760f151172f0)
  307.  
  308. + sct_crop_image -i sub-unf06_T1w_RPI_r.nii.gz -m sub-unf06_T1w_RPI_r_seg_dil.nii.gz
  309.  
  310. --
  311. Spinal Cord Toolbox (git-master-253936cfc07712c587d9f4cfbbcb760f151172f0)
  312.  
  313. Bounding box: x=[81, 110], y=[63, 124], z=[0, 181]
  314. Cropping the image...
  315. + file=sub-unf06_T1w_RPI_r_crop
  316. + sct_crop_image -i sub-unf06_T1w_RPI_r_seg.nii.gz -m sub-unf06_T1w_RPI_r_seg_dil.nii.gz
  317.  
  318. --
  319. Spinal Cord Toolbox (git-master-253936cfc07712c587d9f4cfbbcb760f151172f0)
  320.  
  321. Bounding box: x=[81, 110], y=[63, 124], z=[0, 181]
  322. Cropping the image...
  323. + file_seg=sub-unf06_T1w_RPI_r_seg_crop
  324. + cd ../
  325. + for r_coef in '${R_COEFS[@]}'
  326. + '[' -d anat_r1 ']'
  327. + '[' -f /scratch/jcohen/results_csa_t1_20200824/results/csa_perlevel_sub-unf06_1.csv ']'
  328. + mkdir anat_r1
  329. + cd anat_r1
  330. + file_r=sub-unf06_T1w_RPI_r_crop_r1
  331. + affine_rescale -i ../anat/sub-unf06_T1w_RPI_r_crop.nii.gz -r 1 -o sub-unf06_T1w_RPI_r_crop_r1.nii.gz
  332. + file_label_r=sub-unf06_T1w_RPI_r_crop_r1_seg_labeled
  333. + affine_rescale -i ../anat/sub-unf06_T1w_RPI_r_seg_labeled.nii.gz -r 1 -o sub-unf06_T1w_RPI_r_crop_r1_seg_labeled.nii.gz
  334. ++ seq 3
  335. + seq_transfo='1
  336. 2
  337. 3'
  338. + for i_transfo in '${seq_transfo[@]}'
  339. ++ date +%s
  340. + start=1598284774
  341. + affine_transfo -i sub-unf06_T1w_RPI_r_crop_r1.nii.gz -transfo /scratch/jcohen/results_csa_t1_20200824/results/transfo_values.csv -config /home/jcohen/csa-atrophy/config_script_t1.yml -o _t1
  342. /home/jcohen/csa-atrophy/config_script_t1.yml
  343. error /scratch/jcohen/results_csa_t1_20200824/results/transfo_values.csv is not present in current directory
  344. creating new file named /scratch/jcohen/results_csa_t1_20200824/results/transfo_values.csv
  345.  
  346. ----------affine transformation subject: sub-unf06_T1w_RPI_r_crop_r1.nii.gz------------
  347. min padding: 12
  348. data shape (image with padding): (53, 85, 205)
  349. angles of rotation IS: 1.0147294948978292 PA: 4.069185169325963 LR: 0.17215954206281636
  350. number of pixel shift LR: -0.928893845819897 PA: -0.9456222281688037 IS: -0.9667602118338176
  351. rotation matrix:
  352. [[ 0.99732266 0.0176648 -0.07096099]
  353. [-0.01749618 0.99984244 0.00299717]
  354. [ 0.07100275 -0.0017476 0.99747459]]
  355. new image shape: (53, 85, 205)
  356. new image path: sub-unf06_T1w_RPI_r_crop_r1_t1.nii.gz
  357. + file_r_t=sub-unf06_T1w_RPI_r_crop_r1_t1
  358. ++ date +%s
  359. + end=1598284777
  360. + runtime=3
  361. + echo '+++++++++++ TIME: Duration of of image transfo t1: 0hrs 0min 3sec'
  362. +++++++++++ TIME: Duration of of image transfo t1: 0hrs 0min 3sec
  363. ++ date +%s
  364. + start=1598284777
  365. + affine_transfo -i sub-unf06_T1w_RPI_r_crop_r1_seg_labeled.nii.gz -transfo /scratch/jcohen/results_csa_t1_20200824/results/transfo_values.csv -config /home/jcohen/csa-atrophy/config_script_t1.yml -o _t1 -interpolation 0
  366. /home/jcohen/csa-atrophy/config_script_t1.yml
  367. subjects angle_IS ... shift_PA shift_IS
  368. 0 sub-unf06_T1w_RPI_r_crop_r1_t1 1.014729 ... -0.945622 -0.96676
  369.  
  370. [1 rows x 7 columns]
  371.  
  372. ----------affine transformation subject: sub-unf06_T1w_RPI_r_crop_r1_seg_labeled.nii.gz------------
  373. [ 1.01472949 4.06918517 0.17215954 -0.92889385 -0.94562223 -0.96676021]
  374. min padding: 19
  375. data shape (image with padding): (230, 298, 358)
  376. angles of rotation IS: 1.0147294948978292 PA: 4.069185169325963 LR: 0.17215954206281636
  377. number of pixel shift LR: -0.9288938458198969 PA: -0.9456222281688036 IS: -0.9667602118338176
  378. rotation matrix:
  379. [[ 0.99732266 0.0176648 -0.07096099]
  380. [-0.01749618 0.99984244 0.00299717]
  381. [ 0.07100275 -0.0017476 0.99747459]]
  382. new image shape: (230, 298, 358)
  383. new image path: sub-unf06_T1w_RPI_r_crop_r1_seg_labeled_t1.nii.gz
  384. + file_label_r_t=sub-unf06_T1w_RPI_r_crop_r1_seg_labeled_t1
  385. ++ date +%s
  386. + end=1598284781
  387. + runtime=4
  388. + echo '+++++++++++ TIME: Duration of labelling transfo t1: 0hrs 0min 4sec'
  389. +++++++++++ TIME: Duration of labelling transfo t1: 0hrs 0min 4sec
  390. ++ date +%s
  391. + start=1598284781
  392. + segment_if_does_not_exist sub-unf06_T1w_RPI_r_crop_r1_t1 t1
  393. + local file=sub-unf06_T1w_RPI_r_crop_r1_t1
  394. + local contrast=t1
  395. + local qc=
  396. + FILESEG=sub-unf06_T1w_RPI_r_crop_r1_t1_seg
  397. + FILESEGMANUAL=/home/jcohen/data-multi-subject/derivatives/labels/sub-unf06/anat/sub-unf06_T1w_RPI_r_crop_r1_t1_seg-manual.nii.gz
  398. + '[' -e /home/jcohen/data-multi-subject/derivatives/labels/sub-unf06/anat/sub-unf06_T1w_RPI_r_crop_r1_t1_seg-manual.nii.gz ']'
  399. + sct_deepseg_sc -i sub-unf06_T1w_RPI_r_crop_r1_t1.nii.gz -c t1
  400.  
  401. --
  402. Spinal Cord Toolbox (git-master-253936cfc07712c587d9f4cfbbcb760f151172f0)
  403.  
  404. Config deepseg_sc:
  405. Centerline algorithm: svm
  406. Brain in image: True
  407. Kernel dimension: 2d
  408. Contrast: t1
  409. Threshold: 0.15
  410.  
  411. Create temporary folder (/tmp/sct-20200824115944.453624-qqajhkbp)...
  412. Reorient the image to RPI, if necessary...
  413. Finding the spinal cord centerline...
  414. Remove temporary files...
  415. rm -rf /tmp/sct-20200824115945.612946-sj33k_fe
  416. Cropping the image around the spinal cord...
  417. Normalizing the intensity...
  418. Segmenting the spinal cord using deep learning on 2D patches...
  419. Reassembling the image...
  420. Resampling the segmentation to the native image resolution using linear interpolation...
  421. Binarizing the resampled segmentation...
  422. Found isolated voxels on slice 12, Removing them
  423. Remove temporary files...
  424. rm -rf /tmp/sct-20200824115944.453624-qqajhkbp
  425. ++ date +%s
  426. + end=1598284799
  427. + runtime=18
  428. + echo '+++++++++++ TIME: Duration of segmentation t1: 0hrs 0min 18sec'
  429. +++++++++++ TIME: Duration of segmentation t1: 0hrs 0min 18sec
  430. + file_r_t_seg=sub-unf06_T1w_RPI_r_crop_r1_t1_seg
  431. ++ date +%s
  432. + start=1598284799
  433. + sct_process_segmentation -i sub-unf06_T1w_RPI_r_crop_r1_t1_seg.nii.gz -vert 2:5 -perlevel 1 -vertfile sub-unf06_T1w_RPI_r_crop_r1_seg_labeled_t1.nii.gz -o /scratch/jcohen/results_csa_t1_20200824/results/csa_perlevel_sub-unf06_t1_1.csv
  434.  
  435. --
  436. Spinal Cord Toolbox (git-master-253936cfc07712c587d9f4cfbbcb760f151172f0)
  437.  
  438.  
  439. Done! To view results, type:
  440. xdg-open /scratch/jcohen/results_csa_t1_20200824/results/csa_perlevel_sub-unf06_t1_1.csv
  441.  
  442. ++ date +%s
  443. + end=1598284810
  444. + runtime=11
  445. + echo '+++++++++++ TIME: Duration of sct_process_segmentation t1: 0hrs 0min 11sec'
  446. +++++++++++ TIME: Duration of sct_process_segmentation t1: 0hrs 0min 11sec
  447. + FILES_TO_CHECK+=("$PATH_RESULTS/csa_perlevel_${SUBJECT}_t${i_transfo}_${r_coef}.csv" "$PATH_DATA_PROCESSED/${SUBJECT}/anat_r${r_coef}/${file_r_t}.nii.gz" "$PATH_DATA_PROCESSED/${SUBJECT}/anat_r${r_coef}/${file_r_t_seg}.nii.gz" "$PATH_DATA_PROCESSED/${SUBJECT}/anat_r${r_coef}/${file_label_r_t}.nii.gz")
  448. + for i_transfo in '${seq_transfo[@]}'
  449. ++ date +%s
  450. + start=1598284810
  451. + affine_transfo -i sub-unf06_T1w_RPI_r_crop_r1.nii.gz -transfo /scratch/jcohen/results_csa_t1_20200824/results/transfo_values.csv -config /home/jcohen/csa-atrophy/config_script_t1.yml -o _t2
  452. /home/jcohen/csa-atrophy/config_script_t1.yml
  453. subjects angle_IS ... shift_PA shift_IS
  454. 0 sub-unf06_T1w_RPI_r_crop_r1_t1 1.014729 ... -0.945622 -0.96676
  455.  
  456. [1 rows x 7 columns]
  457.  
  458. ----------affine transformation subject: sub-unf06_T1w_RPI_r_crop_r1.nii.gz------------
  459. min padding: 12
  460. data shape (image with padding): (53, 85, 205)
  461. angles of rotation IS: 0.9502297212101474 PA: 3.133148412586383 LR: 1.8690583233055535
  462. number of pixel shift LR: -0.5218223559038349 PA: -2.298637032844812 IS: -1.3913306427280492
  463. rotation matrix:
  464. [[ 0.9983679 0.01655909 -0.05465651]
  465. [-0.01479265 0.99936009 0.03256668]
  466. [ 0.05516081 -0.03170502 0.99797399]]
  467. new image shape: (53, 85, 205)
  468. new image path: sub-unf06_T1w_RPI_r_crop_r1_t2.nii.gz
  469. + file_r_t=sub-unf06_T1w_RPI_r_crop_r1_t2
  470. ++ date +%s
  471. + end=1598284812
  472. + runtime=2
  473. + echo '+++++++++++ TIME: Duration of of image transfo t2: 0hrs 0min 2sec'
  474. +++++++++++ TIME: Duration of of image transfo t2: 0hrs 0min 2sec
  475. ++ date +%s
  476. + start=1598284812
  477. + affine_transfo -i sub-unf06_T1w_RPI_r_crop_r1_seg_labeled.nii.gz -transfo /scratch/jcohen/results_csa_t1_20200824/results/transfo_values.csv -config /home/jcohen/csa-atrophy/config_script_t1.yml -o _t2 -interpolation 0
  478. /home/jcohen/csa-atrophy/config_script_t1.yml
  479. subjects angle_IS ... shift_PA shift_IS
  480. 0 sub-unf06_T1w_RPI_r_crop_r1_t1 1.014729 ... -0.945622 -0.966760
  481. 1 sub-unf06_T1w_RPI_r_crop_r1_t2 0.950230 ... -2.298637 -1.391331
  482.  
  483. [2 rows x 7 columns]
  484.  
  485. ----------affine transformation subject: sub-unf06_T1w_RPI_r_crop_r1_seg_labeled.nii.gz------------
  486. [ 0.95022972 3.13314841 1.86905832 -0.52182236 -2.29863703 -1.39133064]
  487. min padding: 17
  488. data shape (image with padding): (226, 294, 354)
  489. angles of rotation IS: 0.9502297212101474 PA: 3.133148412586383 LR: 1.869058323305553
  490. number of pixel shift LR: -0.5218223559038349 PA: -2.298637032844812 IS: -1.3913306427280492
  491. rotation matrix:
  492. [[ 0.9983679 0.01655909 -0.05465651]
  493. [-0.01479265 0.99936009 0.03256668]
  494. [ 0.05516081 -0.03170502 0.99797399]]
  495. new image shape: (226, 294, 354)
  496. new image path: sub-unf06_T1w_RPI_r_crop_r1_seg_labeled_t2.nii.gz
  497. + file_label_r_t=sub-unf06_T1w_RPI_r_crop_r1_seg_labeled_t2
  498. ++ date +%s
  499. + end=1598284815
  500. + runtime=3
  501. + echo '+++++++++++ TIME: Duration of labelling transfo t2: 0hrs 0min 3sec'
  502. +++++++++++ TIME: Duration of labelling transfo t2: 0hrs 0min 3sec
  503. ++ date +%s
  504. + start=1598284815
  505. + segment_if_does_not_exist sub-unf06_T1w_RPI_r_crop_r1_t2 t1
  506. + local file=sub-unf06_T1w_RPI_r_crop_r1_t2
  507. + local contrast=t1
  508. + local qc=
  509. + FILESEG=sub-unf06_T1w_RPI_r_crop_r1_t2_seg
  510. + FILESEGMANUAL=/home/jcohen/data-multi-subject/derivatives/labels/sub-unf06/anat/sub-unf06_T1w_RPI_r_crop_r1_t2_seg-manual.nii.gz
  511. + '[' -e /home/jcohen/data-multi-subject/derivatives/labels/sub-unf06/anat/sub-unf06_T1w_RPI_r_crop_r1_t2_seg-manual.nii.gz ']'
  512. + sct_deepseg_sc -i sub-unf06_T1w_RPI_r_crop_r1_t2.nii.gz -c t1
  513.  
  514. --
  515. Spinal Cord Toolbox (git-master-253936cfc07712c587d9f4cfbbcb760f151172f0)
  516.  
  517. Config deepseg_sc:
  518. Centerline algorithm: svm
  519. Brain in image: True
  520. Kernel dimension: 2d
  521. Contrast: t1
  522. Threshold: 0.15
  523.  
  524. Create temporary folder (/tmp/sct-20200824120019.055133-bhnvi8jp)...
  525. Reorient the image to RPI, if necessary...
  526. Finding the spinal cord centerline...
  527. Remove temporary files...
  528. rm -rf /tmp/sct-20200824120020.228546-rhrja68g
  529. Cropping the image around the spinal cord...
  530. Normalizing the intensity...
  531. Segmenting the spinal cord using deep learning on 2D patches...
  532. Reassembling the image...
  533. Resampling the segmentation to the native image resolution using linear interpolation...
  534. Binarizing the resampled segmentation...
  535. Found isolated voxels on slice 10, Removing them
  536. Remove temporary files...
  537. rm -rf /tmp/sct-20200824120019.055133-bhnvi8jp
  538. ++ date +%s
  539. + end=1598284834
  540. + runtime=19
  541. + echo '+++++++++++ TIME: Duration of segmentation t2: 0hrs 0min 19sec'
  542. +++++++++++ TIME: Duration of segmentation t2: 0hrs 0min 19sec
  543. + file_r_t_seg=sub-unf06_T1w_RPI_r_crop_r1_t2_seg
  544. ++ date +%s
  545. + start=1598284834
  546. + sct_process_segmentation -i sub-unf06_T1w_RPI_r_crop_r1_t2_seg.nii.gz -vert 2:5 -perlevel 1 -vertfile sub-unf06_T1w_RPI_r_crop_r1_seg_labeled_t2.nii.gz -o /scratch/jcohen/results_csa_t1_20200824/results/csa_perlevel_sub-unf06_t2_1.csv
  547.  
  548. --
  549. Spinal Cord Toolbox (git-master-253936cfc07712c587d9f4cfbbcb760f151172f0)
  550.  
  551.  
  552. Done! To view results, type:
  553. xdg-open /scratch/jcohen/results_csa_t1_20200824/results/csa_perlevel_sub-unf06_t2_1.csv
  554.  
  555. ++ date +%s
  556. + end=1598284844
  557. + runtime=10
  558. + echo '+++++++++++ TIME: Duration of sct_process_segmentation t2: 0hrs 0min 10sec'
  559. +++++++++++ TIME: Duration of sct_process_segmentation t2: 0hrs 0min 10sec
  560. + FILES_TO_CHECK+=("$PATH_RESULTS/csa_perlevel_${SUBJECT}_t${i_transfo}_${r_coef}.csv" "$PATH_DATA_PROCESSED/${SUBJECT}/anat_r${r_coef}/${file_r_t}.nii.gz" "$PATH_DATA_PROCESSED/${SUBJECT}/anat_r${r_coef}/${file_r_t_seg}.nii.gz" "$PATH_DATA_PROCESSED/${SUBJECT}/anat_r${r_coef}/${file_label_r_t}.nii.gz")
  561. + for i_transfo in '${seq_transfo[@]}'
  562. ++ date +%s
  563. + start=1598284844
  564. + affine_transfo -i sub-unf06_T1w_RPI_r_crop_r1.nii.gz -transfo /scratch/jcohen/results_csa_t1_20200824/results/transfo_values.csv -config /home/jcohen/csa-atrophy/config_script_t1.yml -o _t3
  565. /home/jcohen/csa-atrophy/config_script_t1.yml
  566. subjects angle_IS ... shift_PA shift_IS
  567. 0 sub-unf06_T1w_RPI_r_crop_r1_t1 1.014729 ... -0.945622 -0.966760
  568. 1 sub-unf06_T1w_RPI_r_crop_r1_t2 0.950230 ... -2.298637 -1.391331
  569.  
  570. [2 rows x 7 columns]
  571.  
  572. ----------affine transformation subject: sub-unf06_T1w_RPI_r_crop_r1.nii.gz------------
  573. min padding: 11
  574. data shape (image with padding): (51, 83, 203)
  575. angles of rotation IS: 0.13973713424306422 PA: 3.3397165921697147 LR: -3.823019329505657
  576. number of pixel shift LR: -0.46656751979763655 PA: 0.7140995112739934 IS: -0.47383479363495407
  577. rotation matrix:
  578. [[ 0.99829871 0.00243473 -0.05825605]
  579. [-0.00631764 0.99776232 -0.06656154]
  580. [ 0.05796363 0.06681634 0.99608021]]
  581. new image shape: (51, 83, 203)
  582. new image path: sub-unf06_T1w_RPI_r_crop_r1_t3.nii.gz
  583. + file_r_t=sub-unf06_T1w_RPI_r_crop_r1_t3
  584. ++ date +%s
  585. + end=1598284846
  586. + runtime=2
  587. + echo '+++++++++++ TIME: Duration of of image transfo t3: 0hrs 0min 2sec'
  588. +++++++++++ TIME: Duration of of image transfo t3: 0hrs 0min 2sec
  589. ++ date +%s
  590. + start=1598284846
  591. + affine_transfo -i sub-unf06_T1w_RPI_r_crop_r1_seg_labeled.nii.gz -transfo /scratch/jcohen/results_csa_t1_20200824/results/transfo_values.csv -config /home/jcohen/csa-atrophy/config_script_t1.yml -o _t3 -interpolation 0
  592. /home/jcohen/csa-atrophy/config_script_t1.yml
  593. subjects angle_IS ... shift_PA shift_IS
  594. 0 sub-unf06_T1w_RPI_r_crop_r1_t1 1.014729 ... -0.945622 -0.966760
  595. 1 sub-unf06_T1w_RPI_r_crop_r1_t2 0.950230 ... -2.298637 -1.391331
  596. 2 sub-unf06_T1w_RPI_r_crop_r1_t3 0.139737 ... 0.714100 -0.473835
  597.  
  598. [3 rows x 7 columns]
  599.  
  600. ----------affine transformation subject: sub-unf06_T1w_RPI_r_crop_r1_seg_labeled.nii.gz------------
  601. [ 0.13973713 3.33971659 -3.82301933 -0.46656752 0.71409951 -0.47383479]
  602. min padding: 17
  603. data shape (image with padding): (226, 294, 354)
  604. angles of rotation IS: 0.13973713424306422 PA: 3.3397165921697147 LR: -3.823019329505657
  605. number of pixel shift LR: -0.4665675197976366 PA: 0.7140995112739934 IS: -0.4738347936349541
  606. rotation matrix:
  607. [[ 0.99829871 0.00243473 -0.05825605]
  608. [-0.00631764 0.99776232 -0.06656154]
  609. [ 0.05796363 0.06681634 0.99608021]]
  610. new image shape: (226, 294, 354)
  611. new image path: sub-unf06_T1w_RPI_r_crop_r1_seg_labeled_t3.nii.gz
  612. + file_label_r_t=sub-unf06_T1w_RPI_r_crop_r1_seg_labeled_t3
  613. ++ date +%s
  614. + end=1598284849
  615. + runtime=3
  616. + echo '+++++++++++ TIME: Duration of labelling transfo t3: 0hrs 0min 3sec'
  617. +++++++++++ TIME: Duration of labelling transfo t3: 0hrs 0min 3sec
  618. ++ date +%s
  619. + start=1598284849
  620. + segment_if_does_not_exist sub-unf06_T1w_RPI_r_crop_r1_t3 t1
  621. + local file=sub-unf06_T1w_RPI_r_crop_r1_t3
  622. + local contrast=t1
  623. + local qc=
  624. + FILESEG=sub-unf06_T1w_RPI_r_crop_r1_t3_seg
  625. + FILESEGMANUAL=/home/jcohen/data-multi-subject/derivatives/labels/sub-unf06/anat/sub-unf06_T1w_RPI_r_crop_r1_t3_seg-manual.nii.gz
  626. + '[' -e /home/jcohen/data-multi-subject/derivatives/labels/sub-unf06/anat/sub-unf06_T1w_RPI_r_crop_r1_t3_seg-manual.nii.gz ']'
  627. + sct_deepseg_sc -i sub-unf06_T1w_RPI_r_crop_r1_t3.nii.gz -c t1
  628.  
  629. --
  630. Spinal Cord Toolbox (git-master-253936cfc07712c587d9f4cfbbcb760f151172f0)
  631.  
  632. Config deepseg_sc:
  633. Centerline algorithm: svm
  634. Brain in image: True
  635. Kernel dimension: 2d
  636. Contrast: t1
  637. Threshold: 0.15
  638.  
  639. Create temporary folder (/tmp/sct-20200824120053.227051-1l4bj3yb)...
  640. Reorient the image to RPI, if necessary...
  641. Finding the spinal cord centerline...
  642. Remove temporary files...
  643. rm -rf /tmp/sct-20200824120054.392481-eeh0gynj
  644. Cropping the image around the spinal cord...
  645. Normalizing the intensity...
  646. Segmenting the spinal cord using deep learning on 2D patches...
  647. Reassembling the image...
  648. Resampling the segmentation to the native image resolution using linear interpolation...
  649. Binarizing the resampled segmentation...
  650. Found isolated voxels on slice 13, Removing them
  651. Remove temporary files...
  652. rm -rf /tmp/sct-20200824120053.227051-1l4bj3yb
  653. ++ date +%s
  654. + end=1598284868
  655. + runtime=19
  656. + echo '+++++++++++ TIME: Duration of segmentation t3: 0hrs 0min 19sec'
  657. +++++++++++ TIME: Duration of segmentation t3: 0hrs 0min 19sec
  658. + file_r_t_seg=sub-unf06_T1w_RPI_r_crop_r1_t3_seg
  659. ++ date +%s
  660. + start=1598284868
  661. + sct_process_segmentation -i sub-unf06_T1w_RPI_r_crop_r1_t3_seg.nii.gz -vert 2:5 -perlevel 1 -vertfile sub-unf06_T1w_RPI_r_crop_r1_seg_labeled_t3.nii.gz -o /scratch/jcohen/results_csa_t1_20200824/results/csa_perlevel_sub-unf06_t3_1.csv
  662.  
  663. --
  664. Spinal Cord Toolbox (git-master-253936cfc07712c587d9f4cfbbcb760f151172f0)
  665.  
  666.  
  667. Done! To view results, type:
  668. xdg-open /scratch/jcohen/results_csa_t1_20200824/results/csa_perlevel_sub-unf06_t3_1.csv
  669.  
  670. ++ date +%s
  671. + end=1598284878
  672. + runtime=10
  673. + echo '+++++++++++ TIME: Duration of sct_process_segmentation t3: 0hrs 0min 10sec'
  674. +++++++++++ TIME: Duration of sct_process_segmentation t3: 0hrs 0min 10sec
  675. + FILES_TO_CHECK+=("$PATH_RESULTS/csa_perlevel_${SUBJECT}_t${i_transfo}_${r_coef}.csv" "$PATH_DATA_PROCESSED/${SUBJECT}/anat_r${r_coef}/${file_r_t}.nii.gz" "$PATH_DATA_PROCESSED/${SUBJECT}/anat_r${r_coef}/${file_r_t_seg}.nii.gz" "$PATH_DATA_PROCESSED/${SUBJECT}/anat_r${r_coef}/${file_label_r_t}.nii.gz")
  676. + cd ../
  677. + for r_coef in '${R_COEFS[@]}'
  678. + '[' -d anat_r0.99 ']'
  679. + '[' -f /scratch/jcohen/results_csa_t1_20200824/results/csa_perlevel_sub-unf06_0.99.csv ']'
  680. + mkdir anat_r0.99
  681. + cd anat_r0.99
  682. + file_r=sub-unf06_T1w_RPI_r_crop_r0.99
  683. + affine_rescale -i ../anat/sub-unf06_T1w_RPI_r_crop.nii.gz -r 0.99 -o sub-unf06_T1w_RPI_r_crop_r0.99.nii.gz
  684. + file_label_r=sub-unf06_T1w_RPI_r_crop_r0.99_seg_labeled
  685. + affine_rescale -i ../anat/sub-unf06_T1w_RPI_r_seg_labeled.nii.gz -r 0.99 -o sub-unf06_T1w_RPI_r_crop_r0.99_seg_labeled.nii.gz
  686. ++ seq 3
  687. + seq_transfo='1
  688. 2
  689. 3'
  690. + for i_transfo in '${seq_transfo[@]}'
  691. ++ date +%s
  692. + start=1598284880
  693. + affine_transfo -i sub-unf06_T1w_RPI_r_crop_r0.99.nii.gz -transfo /scratch/jcohen/results_csa_t1_20200824/results/transfo_values.csv -config /home/jcohen/csa-atrophy/config_script_t1.yml -o _t1
  694. /home/jcohen/csa-atrophy/config_script_t1.yml
  695. subjects angle_IS ... shift_PA shift_IS
  696. 0 sub-unf06_T1w_RPI_r_crop_r1_t1 1.014729 ... -0.945622 -0.966760
  697. 1 sub-unf06_T1w_RPI_r_crop_r1_t2 0.950230 ... -2.298637 -1.391331
  698. 2 sub-unf06_T1w_RPI_r_crop_r1_t3 0.139737 ... 0.714100 -0.473835
  699.  
  700. [3 rows x 7 columns]
  701.  
  702. ----------affine transformation subject: sub-unf06_T1w_RPI_r_crop_r0.99.nii.gz------------
  703. min padding: 15
  704. data shape (image with padding): (59, 91, 211)
  705. angles of rotation IS: -4.9535057934310425 PA: -1.5208746228765413 LR: -4.087507788654044
  706. number of pixel shift LR: -1.7253999638572965 PA: -1.8723482978172217 IS: 0.262686820980052
  707. rotation matrix:
  708. [[ 0.99591413 -0.08631691 0.02654115]
  709. [ 0.08801247 0.99356759 -0.07125486]
  710. [-0.02021993 0.07329967 0.99710497]]
  711. new image shape: (59, 91, 211)
  712. new image path: sub-unf06_T1w_RPI_r_crop_r0.99_t1.nii.gz
  713. + file_r_t=sub-unf06_T1w_RPI_r_crop_r0.99_t1
  714. ++ date +%s
  715. + end=1598284882
  716. + runtime=2
  717. + echo '+++++++++++ TIME: Duration of of image transfo t1: 0hrs 0min 2sec'
  718. +++++++++++ TIME: Duration of of image transfo t1: 0hrs 0min 2sec
  719. ++ date +%s
  720. + start=1598284882
  721. + affine_transfo -i sub-unf06_T1w_RPI_r_crop_r0.99_seg_labeled.nii.gz -transfo /scratch/jcohen/results_csa_t1_20200824/results/transfo_values.csv -config /home/jcohen/csa-atrophy/config_script_t1.yml -o _t1 -interpolation 0
  722. /home/jcohen/csa-atrophy/config_script_t1.yml
  723. subjects angle_IS ... shift_PA shift_IS
  724. 0 sub-unf06_T1w_RPI_r_crop_r1_t1 1.014729 ... -0.945622 -0.966760
  725. 1 sub-unf06_T1w_RPI_r_crop_r1_t2 0.950230 ... -2.298637 -1.391331
  726. 2 sub-unf06_T1w_RPI_r_crop_r1_t3 0.139737 ... 0.714100 -0.473835
  727. 3 sub-unf06_T1w_RPI_r_crop_r0.99_t1 -4.953506 ... -1.872348 0.262687
  728.  
  729. [4 rows x 7 columns]
  730.  
  731. ----------affine transformation subject: sub-unf06_T1w_RPI_r_crop_r0.99_seg_labeled.nii.gz------------
  732. [-4.95350579 -1.52087462 -4.08750779 -1.72539996 -1.8723483 0.26268682]
  733. min padding: 24
  734. data shape (image with padding): (240, 308, 368)
  735. angles of rotation IS: -4.9535057934310425 PA: -1.5208746228765413 LR: -4.087507788654044
  736. number of pixel shift LR: -1.7253999638572963 PA: -1.8723482978172217 IS: 0.262686820980052
  737. rotation matrix:
  738. [[ 0.99591413 -0.08631691 0.02654115]
  739. [ 0.08801247 0.99356759 -0.07125486]
  740. [-0.02021993 0.07329967 0.99710497]]
  741. new image shape: (240, 308, 368)
  742. new image path: sub-unf06_T1w_RPI_r_crop_r0.99_seg_labeled_t1.nii.gz
  743. + file_label_r_t=sub-unf06_T1w_RPI_r_crop_r0.99_seg_labeled_t1
  744. ++ date +%s
  745. + end=1598284886
  746. + runtime=4
  747. + echo '+++++++++++ TIME: Duration of labelling transfo t1: 0hrs 0min 4sec'
  748. +++++++++++ TIME: Duration of labelling transfo t1: 0hrs 0min 4sec
  749. ++ date +%s
  750. + start=1598284886
  751. + segment_if_does_not_exist sub-unf06_T1w_RPI_r_crop_r0.99_t1 t1
  752. + local file=sub-unf06_T1w_RPI_r_crop_r0.99_t1
  753. + local contrast=t1
  754. + local qc=
  755. + FILESEG=sub-unf06_T1w_RPI_r_crop_r0.99_t1_seg
  756. + FILESEGMANUAL=/home/jcohen/data-multi-subject/derivatives/labels/sub-unf06/anat/sub-unf06_T1w_RPI_r_crop_r0.99_t1_seg-manual.nii.gz
  757. + '[' -e /home/jcohen/data-multi-subject/derivatives/labels/sub-unf06/anat/sub-unf06_T1w_RPI_r_crop_r0.99_t1_seg-manual.nii.gz ']'
  758. + sct_deepseg_sc -i sub-unf06_T1w_RPI_r_crop_r0.99_t1.nii.gz -c t1
  759.  
  760. --
  761. Spinal Cord Toolbox (git-master-253936cfc07712c587d9f4cfbbcb760f151172f0)
  762.  
  763. Config deepseg_sc:
  764. Centerline algorithm: svm
  765. Brain in image: True
  766. Kernel dimension: 2d
  767. Contrast: t1
  768. Threshold: 0.15
  769.  
  770. Create temporary folder (/tmp/sct-20200824120129.857126-btlg3mak)...
  771. Reorient the image to RPI, if necessary...
  772. Finding the spinal cord centerline...
  773. Remove temporary files...
  774. rm -rf /tmp/sct-20200824120131.133600-nwnb5n41
  775. Cropping the image around the spinal cord...
  776. Normalizing the intensity...
  777. Segmenting the spinal cord using deep learning on 2D patches...
  778. Reassembling the image...
  779. Resampling the segmentation to the native image resolution using linear interpolation...
  780. Binarizing the resampled segmentation...
  781. Removing small objects above slice #187
  782. Found isolated voxels on slice 17, Removing them
  783. Remove temporary files...
  784. rm -rf /tmp/sct-20200824120129.857126-btlg3mak
  785. ++ date +%s
  786. + end=1598284905
  787. + runtime=19
  788. + echo '+++++++++++ TIME: Duration of segmentation t1: 0hrs 0min 19sec'
  789. +++++++++++ TIME: Duration of segmentation t1: 0hrs 0min 19sec
  790. + file_r_t_seg=sub-unf06_T1w_RPI_r_crop_r0.99_t1_seg
  791. ++ date +%s
  792. + start=1598284905
  793. + sct_process_segmentation -i sub-unf06_T1w_RPI_r_crop_r0.99_t1_seg.nii.gz -vert 2:5 -perlevel 1 -vertfile sub-unf06_T1w_RPI_r_crop_r0.99_seg_labeled_t1.nii.gz -o /scratch/jcohen/results_csa_t1_20200824/results/csa_perlevel_sub-unf06_t1_0.99.csv
  794.  
  795. --
  796. Spinal Cord Toolbox (git-master-253936cfc07712c587d9f4cfbbcb760f151172f0)
  797.  
  798.  
  799. Done! To view results, type:
  800. xdg-open /scratch/jcohen/results_csa_t1_20200824/results/csa_perlevel_sub-unf06_t1_0.99.csv
  801.  
  802. ++ date +%s
  803. + end=1598284916
  804. + runtime=11
  805. + echo '+++++++++++ TIME: Duration of sct_process_segmentation t1: 0hrs 0min 11sec'
  806. +++++++++++ TIME: Duration of sct_process_segmentation t1: 0hrs 0min 11sec
  807. + FILES_TO_CHECK+=("$PATH_RESULTS/csa_perlevel_${SUBJECT}_t${i_transfo}_${r_coef}.csv" "$PATH_DATA_PROCESSED/${SUBJECT}/anat_r${r_coef}/${file_r_t}.nii.gz" "$PATH_DATA_PROCESSED/${SUBJECT}/anat_r${r_coef}/${file_r_t_seg}.nii.gz" "$PATH_DATA_PROCESSED/${SUBJECT}/anat_r${r_coef}/${file_label_r_t}.nii.gz")
  808. + for i_transfo in '${seq_transfo[@]}'
  809. ++ date +%s
  810. + start=1598284916
  811. + affine_transfo -i sub-unf06_T1w_RPI_r_crop_r0.99.nii.gz -transfo /scratch/jcohen/results_csa_t1_20200824/results/transfo_values.csv -config /home/jcohen/csa-atrophy/config_script_t1.yml -o _t2
  812. /home/jcohen/csa-atrophy/config_script_t1.yml
  813. subjects angle_IS ... shift_PA shift_IS
  814. 0 sub-unf06_T1w_RPI_r_crop_r1_t1 1.014729 ... -0.945622 -0.966760
  815. 1 sub-unf06_T1w_RPI_r_crop_r1_t2 0.950230 ... -2.298637 -1.391331
  816. 2 sub-unf06_T1w_RPI_r_crop_r1_t3 0.139737 ... 0.714100 -0.473835
  817. 3 sub-unf06_T1w_RPI_r_crop_r0.99_t1 -4.953506 ... -1.872348 0.262687
  818.  
  819. [4 rows x 7 columns]
  820.  
  821. ----------affine transformation subject: sub-unf06_T1w_RPI_r_crop_r0.99.nii.gz------------
  822. min padding: 14
  823. data shape (image with padding): (57, 89, 209)
  824. angles of rotation IS: 4.770791246041469 PA: -3.5411216126031575 LR: -3.062796328020827
  825. number of pixel shift LR: 0.2765008022644977 PA: 1.1462728919039673 IS: -1.3383387656440187
  826. rotation matrix:
  827. [[ 0.99463273 0.08301104 0.06176489]
  828. [-0.07976234 0.99538638 -0.05332841]
  829. [-0.06590678 0.04811567 0.99666503]]
  830. new image shape: (57, 89, 209)
  831. new image path: sub-unf06_T1w_RPI_r_crop_r0.99_t2.nii.gz
  832. + file_r_t=sub-unf06_T1w_RPI_r_crop_r0.99_t2
  833. ++ date +%s
  834. + end=1598284918
  835. + runtime=2
  836. + echo '+++++++++++ TIME: Duration of of image transfo t2: 0hrs 0min 2sec'
  837. +++++++++++ TIME: Duration of of image transfo t2: 0hrs 0min 2sec
  838. ++ date +%s
  839. + start=1598284918
  840. + affine_transfo -i sub-unf06_T1w_RPI_r_crop_r0.99_seg_labeled.nii.gz -transfo /scratch/jcohen/results_csa_t1_20200824/results/transfo_values.csv -config /home/jcohen/csa-atrophy/config_script_t1.yml -o _t2 -interpolation 0
  841. /home/jcohen/csa-atrophy/config_script_t1.yml
  842. subjects angle_IS ... shift_PA shift_IS
  843. 0 sub-unf06_T1w_RPI_r_crop_r1_t1 1.014729 ... -0.945622 -0.966760
  844. 1 sub-unf06_T1w_RPI_r_crop_r1_t2 0.950230 ... -2.298637 -1.391331
  845. 2 sub-unf06_T1w_RPI_r_crop_r1_t3 0.139737 ... 0.714100 -0.473835
  846. 3 sub-unf06_T1w_RPI_r_crop_r0.99_t1 -4.953506 ... -1.872348 0.262687
  847. 4 sub-unf06_T1w_RPI_r_crop_r0.99_t2 4.770791 ... 1.146273 -1.338339
  848.  
  849. [5 rows x 7 columns]
  850.  
  851. ----------affine transformation subject: sub-unf06_T1w_RPI_r_crop_r0.99_seg_labeled.nii.gz------------
  852. [ 4.77079125 -3.54112161 -3.06279633 0.2765008 1.14627289 -1.33833877]
  853. min padding: 22
  854. data shape (image with padding): (236, 304, 364)
  855. angles of rotation IS: 4.770791246041469 PA: -3.541121612603157 LR: -3.0627963280208266
  856. number of pixel shift LR: 0.2765008022644977 PA: 1.1462728919039673 IS: -1.3383387656440189
  857. rotation matrix:
  858. [[ 0.99463273 0.08301104 0.06176489]
  859. [-0.07976234 0.99538638 -0.05332841]
  860. [-0.06590678 0.04811567 0.99666503]]
  861. new image shape: (236, 304, 364)
  862. new image path: sub-unf06_T1w_RPI_r_crop_r0.99_seg_labeled_t2.nii.gz
  863. + file_label_r_t=sub-unf06_T1w_RPI_r_crop_r0.99_seg_labeled_t2
  864. ++ date +%s
  865. + end=1598284922
  866. + runtime=4
  867. + echo '+++++++++++ TIME: Duration of labelling transfo t2: 0hrs 0min 4sec'
  868. +++++++++++ TIME: Duration of labelling transfo t2: 0hrs 0min 4sec
  869. ++ date +%s
  870. + start=1598284922
  871. + segment_if_does_not_exist sub-unf06_T1w_RPI_r_crop_r0.99_t2 t1
  872. + local file=sub-unf06_T1w_RPI_r_crop_r0.99_t2
  873. + local contrast=t1
  874. + local qc=
  875. + FILESEG=sub-unf06_T1w_RPI_r_crop_r0.99_t2_seg
  876. + FILESEGMANUAL=/home/jcohen/data-multi-subject/derivatives/labels/sub-unf06/anat/sub-unf06_T1w_RPI_r_crop_r0.99_t2_seg-manual.nii.gz
  877. + '[' -e /home/jcohen/data-multi-subject/derivatives/labels/sub-unf06/anat/sub-unf06_T1w_RPI_r_crop_r0.99_t2_seg-manual.nii.gz ']'
  878. + sct_deepseg_sc -i sub-unf06_T1w_RPI_r_crop_r0.99_t2.nii.gz -c t1
  879.  
  880. --
  881. Spinal Cord Toolbox (git-master-253936cfc07712c587d9f4cfbbcb760f151172f0)
  882.  
  883. Config deepseg_sc:
  884. Centerline algorithm: svm
  885. Brain in image: True
  886. Kernel dimension: 2d
  887. Contrast: t1
  888. Threshold: 0.15
  889.  
  890. Create temporary folder (/tmp/sct-20200824120206.133607-umnmn9ce)...
  891. Reorient the image to RPI, if necessary...
  892. Finding the spinal cord centerline...
  893. Remove temporary files...
  894. rm -rf /tmp/sct-20200824120207.333446-rdv7oylo
  895. Cropping the image around the spinal cord...
  896. Normalizing the intensity...
  897. Segmenting the spinal cord using deep learning on 2D patches...
  898. Reassembling the image...
  899. Resampling the segmentation to the native image resolution using linear interpolation...
  900. Binarizing the resampled segmentation...
  901. Removing small objects above slice #185
  902. Found isolated voxels on slice 15, Removing them
  903. Remove temporary files...
  904. rm -rf /tmp/sct-20200824120206.133607-umnmn9ce
  905. ++ date +%s
  906. + end=1598284941
  907. + runtime=19
  908. + echo '+++++++++++ TIME: Duration of segmentation t2: 0hrs 0min 19sec'
  909. +++++++++++ TIME: Duration of segmentation t2: 0hrs 0min 19sec
  910. + file_r_t_seg=sub-unf06_T1w_RPI_r_crop_r0.99_t2_seg
  911. ++ date +%s
  912. + start=1598284941
  913. + sct_process_segmentation -i sub-unf06_T1w_RPI_r_crop_r0.99_t2_seg.nii.gz -vert 2:5 -perlevel 1 -vertfile sub-unf06_T1w_RPI_r_crop_r0.99_seg_labeled_t2.nii.gz -o /scratch/jcohen/results_csa_t1_20200824/results/csa_perlevel_sub-unf06_t2_0.99.csv
  914.  
  915. --
  916. Spinal Cord Toolbox (git-master-253936cfc07712c587d9f4cfbbcb760f151172f0)
  917.  
  918.  
  919. Done! To view results, type:
  920. xdg-open /scratch/jcohen/results_csa_t1_20200824/results/csa_perlevel_sub-unf06_t2_0.99.csv
  921.  
  922. ++ date +%s
  923. + end=1598284952
  924. + runtime=11
  925. + echo '+++++++++++ TIME: Duration of sct_process_segmentation t2: 0hrs 0min 11sec'
  926. +++++++++++ TIME: Duration of sct_process_segmentation t2: 0hrs 0min 11sec
  927. + FILES_TO_CHECK+=("$PATH_RESULTS/csa_perlevel_${SUBJECT}_t${i_transfo}_${r_coef}.csv" "$PATH_DATA_PROCESSED/${SUBJECT}/anat_r${r_coef}/${file_r_t}.nii.gz" "$PATH_DATA_PROCESSED/${SUBJECT}/anat_r${r_coef}/${file_r_t_seg}.nii.gz" "$PATH_DATA_PROCESSED/${SUBJECT}/anat_r${r_coef}/${file_label_r_t}.nii.gz")
  928. + for i_transfo in '${seq_transfo[@]}'
  929. ++ date +%s
  930. + start=1598284952
  931. + affine_transfo -i sub-unf06_T1w_RPI_r_crop_r0.99.nii.gz -transfo /scratch/jcohen/results_csa_t1_20200824/results/transfo_values.csv -config /home/jcohen/csa-atrophy/config_script_t1.yml -o _t3
  932. /home/jcohen/csa-atrophy/config_script_t1.yml
  933. subjects angle_IS ... shift_PA shift_IS
  934. 0 sub-unf06_T1w_RPI_r_crop_r1_t1 1.014729 ... -0.945622 -0.966760
  935. 1 sub-unf06_T1w_RPI_r_crop_r1_t2 0.950230 ... -2.298637 -1.391331
  936. 2 sub-unf06_T1w_RPI_r_crop_r1_t3 0.139737 ... 0.714100 -0.473835
  937. 3 sub-unf06_T1w_RPI_r_crop_r0.99_t1 -4.953506 ... -1.872348 0.262687
  938. 4 sub-unf06_T1w_RPI_r_crop_r0.99_t2 4.770791 ... 1.146273 -1.338339
  939.  
  940. [5 rows x 7 columns]
  941.  
  942. ----------affine transformation subject: sub-unf06_T1w_RPI_r_crop_r0.99.nii.gz------------
  943. min padding: 15
  944. data shape (image with padding): (59, 91, 211)
  945. angles of rotation IS: -4.204389143138094 PA: 2.9509432255613954 LR: 4.585272987567009
  946. number of pixel shift LR: 0.5251689807739296 PA: -0.5420044863829454 IS: 2.4734709768066425
  947. rotation matrix:
  948. [[ 0.99598641 -0.07321738 -0.05148091]
  949. [ 0.0771844 0.99381521 0.07983671]
  950. [ 0.04531708 -0.0834898 0.99547768]]
  951. new image shape: (59, 91, 211)
  952. new image path: sub-unf06_T1w_RPI_r_crop_r0.99_t3.nii.gz
  953. + file_r_t=sub-unf06_T1w_RPI_r_crop_r0.99_t3
  954. ++ date +%s
  955. + end=1598284954
  956. + runtime=2
  957. + echo '+++++++++++ TIME: Duration of of image transfo t3: 0hrs 0min 2sec'
  958. +++++++++++ TIME: Duration of of image transfo t3: 0hrs 0min 2sec
  959. ++ date +%s
  960. + start=1598284954
  961. + affine_transfo -i sub-unf06_T1w_RPI_r_crop_r0.99_seg_labeled.nii.gz -transfo /scratch/jcohen/results_csa_t1_20200824/results/transfo_values.csv -config /home/jcohen/csa-atrophy/config_script_t1.yml -o _t3 -interpolation 0
  962. /home/jcohen/csa-atrophy/config_script_t1.yml
  963. subjects angle_IS ... shift_PA shift_IS
  964. 0 sub-unf06_T1w_RPI_r_crop_r1_t1 1.014729 ... -0.945622 -0.966760
  965. 1 sub-unf06_T1w_RPI_r_crop_r1_t2 0.950230 ... -2.298637 -1.391331
  966. 2 sub-unf06_T1w_RPI_r_crop_r1_t3 0.139737 ... 0.714100 -0.473835
  967. 3 sub-unf06_T1w_RPI_r_crop_r0.99_t1 -4.953506 ... -1.872348 0.262687
  968. 4 sub-unf06_T1w_RPI_r_crop_r0.99_t2 4.770791 ... 1.146273 -1.338339
  969. 5 sub-unf06_T1w_RPI_r_crop_r0.99_t3 -4.204389 ... -0.542004 2.473471
  970.  
  971. [6 rows x 7 columns]
  972.  
  973. ----------affine transformation subject: sub-unf06_T1w_RPI_r_crop_r0.99_seg_labeled.nii.gz------------
  974. [-4.20438914 2.95094323 4.58527299 0.52516898 -0.54200449 2.47347098]
  975. min padding: 24
  976. data shape (image with padding): (240, 308, 368)
  977. angles of rotation IS: -4.204389143138094 PA: 2.9509432255613954 LR: 4.585272987567008
  978. number of pixel shift LR: 0.5251689807739296 PA: -0.5420044863829454 IS: 2.4734709768066425
  979. rotation matrix:
  980. [[ 0.99598641 -0.07321738 -0.05148091]
  981. [ 0.0771844 0.99381521 0.07983671]
  982. [ 0.04531708 -0.0834898 0.99547768]]
  983. new image shape: (240, 308, 368)
  984. new image path: sub-unf06_T1w_RPI_r_crop_r0.99_seg_labeled_t3.nii.gz
  985. + file_label_r_t=sub-unf06_T1w_RPI_r_crop_r0.99_seg_labeled_t3
  986. ++ date +%s
  987. + end=1598284958
  988. + runtime=4
  989. + echo '+++++++++++ TIME: Duration of labelling transfo t3: 0hrs 0min 4sec'
  990. +++++++++++ TIME: Duration of labelling transfo t3: 0hrs 0min 4sec
  991. ++ date +%s
  992. + start=1598284958
  993. + segment_if_does_not_exist sub-unf06_T1w_RPI_r_crop_r0.99_t3 t1
  994. + local file=sub-unf06_T1w_RPI_r_crop_r0.99_t3
  995. + local contrast=t1
  996. + local qc=
  997. + FILESEG=sub-unf06_T1w_RPI_r_crop_r0.99_t3_seg
  998. + FILESEGMANUAL=/home/jcohen/data-multi-subject/derivatives/labels/sub-unf06/anat/sub-unf06_T1w_RPI_r_crop_r0.99_t3_seg-manual.nii.gz
  999. + '[' -e /home/jcohen/data-multi-subject/derivatives/labels/sub-unf06/anat/sub-unf06_T1w_RPI_r_crop_r0.99_t3_seg-manual.nii.gz ']'
  1000. + sct_deepseg_sc -i sub-unf06_T1w_RPI_r_crop_r0.99_t3.nii.gz -c t1
  1001.  
  1002. --
  1003. Spinal Cord Toolbox (git-master-253936cfc07712c587d9f4cfbbcb760f151172f0)
  1004.  
  1005. Config deepseg_sc:
  1006. Centerline algorithm: svm
  1007. Brain in image: True
  1008. Kernel dimension: 2d
  1009. Contrast: t1
  1010. Threshold: 0.15
  1011.  
  1012. Create temporary folder (/tmp/sct-20200824120242.004760-84s3q4n5)...
  1013. Reorient the image to RPI, if necessary...
  1014. Finding the spinal cord centerline...
  1015. Remove temporary files...
  1016. rm -rf /tmp/sct-20200824120243.249478-fvo8due8
  1017. Cropping the image around the spinal cord...
  1018. Normalizing the intensity...
  1019. Segmenting the spinal cord using deep learning on 2D patches...
  1020. Reassembling the image...
  1021. Resampling the segmentation to the native image resolution using linear interpolation...
  1022. Binarizing the resampled segmentation...
  1023. Found isolated voxels on slice 17, Removing them
  1024. Remove temporary files...
  1025. rm -rf /tmp/sct-20200824120242.004760-84s3q4n5
  1026. ++ date +%s
  1027. + end=1598284977
  1028. + runtime=19
  1029. + echo '+++++++++++ TIME: Duration of segmentation t3: 0hrs 0min 19sec'
  1030. +++++++++++ TIME: Duration of segmentation t3: 0hrs 0min 19sec
  1031. + file_r_t_seg=sub-unf06_T1w_RPI_r_crop_r0.99_t3_seg
  1032. ++ date +%s
  1033. + start=1598284977
  1034. + sct_process_segmentation -i sub-unf06_T1w_RPI_r_crop_r0.99_t3_seg.nii.gz -vert 2:5 -perlevel 1 -vertfile sub-unf06_T1w_RPI_r_crop_r0.99_seg_labeled_t3.nii.gz -o /scratch/jcohen/results_csa_t1_20200824/results/csa_perlevel_sub-unf06_t3_0.99.csv
  1035.  
  1036. --
  1037. Spinal Cord Toolbox (git-master-253936cfc07712c587d9f4cfbbcb760f151172f0)
  1038.  
  1039.  
  1040. Done! To view results, type:
  1041. xdg-open /scratch/jcohen/results_csa_t1_20200824/results/csa_perlevel_sub-unf06_t3_0.99.csv
  1042.  
  1043. ++ date +%s
  1044. + end=1598284988
  1045. + runtime=11
  1046. + echo '+++++++++++ TIME: Duration of sct_process_segmentation t3: 0hrs 0min 11sec'
  1047. +++++++++++ TIME: Duration of sct_process_segmentation t3: 0hrs 0min 11sec
  1048. + FILES_TO_CHECK+=("$PATH_RESULTS/csa_perlevel_${SUBJECT}_t${i_transfo}_${r_coef}.csv" "$PATH_DATA_PROCESSED/${SUBJECT}/anat_r${r_coef}/${file_r_t}.nii.gz" "$PATH_DATA_PROCESSED/${SUBJECT}/anat_r${r_coef}/${file_r_t_seg}.nii.gz" "$PATH_DATA_PROCESSED/${SUBJECT}/anat_r${r_coef}/${file_label_r_t}.nii.gz")
  1049. + cd ../
  1050. + for file in '${FILES_TO_CHECK[@]}'
  1051. + '[' '!' -e /scratch/jcohen/results_csa_t1_20200824/results/csa_perlevel_sub-unf06_t1_1.csv ']'
  1052. + for file in '${FILES_TO_CHECK[@]}'
  1053. + '[' '!' -e /scratch/jcohen/results_csa_t1_20200824/data_processed/sub-unf06/anat_r1/sub-unf06_T1w_RPI_r_crop_r1_t1.nii.gz ']'
  1054. + for file in '${FILES_TO_CHECK[@]}'
  1055. + '[' '!' -e /scratch/jcohen/results_csa_t1_20200824/data_processed/sub-unf06/anat_r1/sub-unf06_T1w_RPI_r_crop_r1_t1_seg.nii.gz ']'
  1056. + for file in '${FILES_TO_CHECK[@]}'
  1057. + '[' '!' -e /scratch/jcohen/results_csa_t1_20200824/data_processed/sub-unf06/anat_r1/sub-unf06_T1w_RPI_r_crop_r1_seg_labeled_t1.nii.gz ']'
  1058. + for file in '${FILES_TO_CHECK[@]}'
  1059. + '[' '!' -e /scratch/jcohen/results_csa_t1_20200824/results/csa_perlevel_sub-unf06_t2_1.csv ']'
  1060. + for file in '${FILES_TO_CHECK[@]}'
  1061. + '[' '!' -e /scratch/jcohen/results_csa_t1_20200824/data_processed/sub-unf06/anat_r1/sub-unf06_T1w_RPI_r_crop_r1_t2.nii.gz ']'
  1062. + for file in '${FILES_TO_CHECK[@]}'
  1063. + '[' '!' -e /scratch/jcohen/results_csa_t1_20200824/data_processed/sub-unf06/anat_r1/sub-unf06_T1w_RPI_r_crop_r1_t2_seg.nii.gz ']'
  1064. + for file in '${FILES_TO_CHECK[@]}'
  1065. + '[' '!' -e /scratch/jcohen/results_csa_t1_20200824/data_processed/sub-unf06/anat_r1/sub-unf06_T1w_RPI_r_crop_r1_seg_labeled_t2.nii.gz ']'
  1066. + for file in '${FILES_TO_CHECK[@]}'
  1067. + '[' '!' -e /scratch/jcohen/results_csa_t1_20200824/results/csa_perlevel_sub-unf06_t3_1.csv ']'
  1068. + for file in '${FILES_TO_CHECK[@]}'
  1069. + '[' '!' -e /scratch/jcohen/results_csa_t1_20200824/data_processed/sub-unf06/anat_r1/sub-unf06_T1w_RPI_r_crop_r1_t3.nii.gz ']'
  1070. + for file in '${FILES_TO_CHECK[@]}'
  1071. + '[' '!' -e /scratch/jcohen/results_csa_t1_20200824/data_processed/sub-unf06/anat_r1/sub-unf06_T1w_RPI_r_crop_r1_t3_seg.nii.gz ']'
  1072. + for file in '${FILES_TO_CHECK[@]}'
  1073. + '[' '!' -e /scratch/jcohen/results_csa_t1_20200824/data_processed/sub-unf06/anat_r1/sub-unf06_T1w_RPI_r_crop_r1_seg_labeled_t3.nii.gz ']'
  1074. + for file in '${FILES_TO_CHECK[@]}'
  1075. + '[' '!' -e /scratch/jcohen/results_csa_t1_20200824/results/csa_perlevel_sub-unf06_t1_0.99.csv ']'
  1076. + for file in '${FILES_TO_CHECK[@]}'
  1077. + '[' '!' -e /scratch/jcohen/results_csa_t1_20200824/data_processed/sub-unf06/anat_r0.99/sub-unf06_T1w_RPI_r_crop_r0.99_t1.nii.gz ']'
  1078. + for file in '${FILES_TO_CHECK[@]}'
  1079. + '[' '!' -e /scratch/jcohen/results_csa_t1_20200824/data_processed/sub-unf06/anat_r0.99/sub-unf06_T1w_RPI_r_crop_r0.99_t1_seg.nii.gz ']'
  1080. + for file in '${FILES_TO_CHECK[@]}'
  1081. + '[' '!' -e /scratch/jcohen/results_csa_t1_20200824/data_processed/sub-unf06/anat_r0.99/sub-unf06_T1w_RPI_r_crop_r0.99_seg_labeled_t1.nii.gz ']'
  1082. + for file in '${FILES_TO_CHECK[@]}'
  1083. + '[' '!' -e /scratch/jcohen/results_csa_t1_20200824/results/csa_perlevel_sub-unf06_t2_0.99.csv ']'
  1084. + for file in '${FILES_TO_CHECK[@]}'
  1085. + '[' '!' -e /scratch/jcohen/results_csa_t1_20200824/data_processed/sub-unf06/anat_r0.99/sub-unf06_T1w_RPI_r_crop_r0.99_t2.nii.gz ']'
  1086. + for file in '${FILES_TO_CHECK[@]}'
  1087. + '[' '!' -e /scratch/jcohen/results_csa_t1_20200824/data_processed/sub-unf06/anat_r0.99/sub-unf06_T1w_RPI_r_crop_r0.99_t2_seg.nii.gz ']'
  1088. + for file in '${FILES_TO_CHECK[@]}'
  1089. + '[' '!' -e /scratch/jcohen/results_csa_t1_20200824/data_processed/sub-unf06/anat_r0.99/sub-unf06_T1w_RPI_r_crop_r0.99_seg_labeled_t2.nii.gz ']'
  1090. + for file in '${FILES_TO_CHECK[@]}'
  1091. + '[' '!' -e /scratch/jcohen/results_csa_t1_20200824/results/csa_perlevel_sub-unf06_t3_0.99.csv ']'
  1092. + for file in '${FILES_TO_CHECK[@]}'
  1093. + '[' '!' -e /scratch/jcohen/results_csa_t1_20200824/data_processed/sub-unf06/anat_r0.99/sub-unf06_T1w_RPI_r_crop_r0.99_t3.nii.gz ']'
  1094. + for file in '${FILES_TO_CHECK[@]}'
  1095. + '[' '!' -e /scratch/jcohen/results_csa_t1_20200824/data_processed/sub-unf06/anat_r0.99/sub-unf06_T1w_RPI_r_crop_r0.99_t3_seg.nii.gz ']'
  1096. + for file in '${FILES_TO_CHECK[@]}'
  1097. + '[' '!' -e /scratch/jcohen/results_csa_t1_20200824/data_processed/sub-unf06/anat_r0.99/sub-unf06_T1w_RPI_r_crop_r0.99_seg_labeled_t3.nii.gz ']'
  1098. ++ date +%s
  1099. + end=1598284988
  1100. + runtime=11
  1101. + echo
  1102.  
  1103. + echo '~~~'
  1104. ~~~
  1105. ++ sct_version
  1106. + echo 'SCT version: git-master-253936cfc07712c587d9f4cfbbcb760f151172f0'
  1107. SCT version: git-master-253936cfc07712c587d9f4cfbbcb760f151172f0
  1108. ++ uname -nsr
  1109. + echo 'Ran on: Linux gra824 3.10.0-1127.8.2.el7.x86_64'
  1110. Ran on: Linux gra824 3.10.0-1127.8.2.el7.x86_64
  1111. + echo 'Duration: 0hrs 0min 11sec'
  1112. Duration: 0hrs 0min 11sec
  1113. + echo '~~~'
  1114. ~~~
  1115.  
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