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recon-all.cmd

recon-all.cmd 29 KB
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  1. 

  2. 

  3. #---------------------------------
    4. 

  4. # New invocation of recon-all Wed Oct 16 15:51:17 UTC 2019 
    5. 

  5. 

  6.  mri_convert /scratch/03763/oesteban/fmriprep-work/sub-03/fmriprep_wf/single_subject_03_wf/anat_preproc_wf/anat_template_wf/t1_merge/sub-03_ses-retest_T1w_template.nii.gz /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-03/mri/orig/001.mgz 
    7. 

  7. 

  8. #--------------------------------------------
    9. 

  9. #@# MotionCor Wed Oct 16 15:51:29 UTC 2019
    10. 

  10. 

  11.  cp /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-03/mri/orig/001.mgz /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-03/mri/rawavg.mgz 
    12. 

  12. 

  13. 

  14.  mri_convert /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-03/mri/rawavg.mgz /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-03/mri/orig.mgz --conform 
    15. 

  15. 

  16. 

  17.  mri_add_xform_to_header -c /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-03/mri/transforms/talairach.xfm /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-03/mri/orig.mgz /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-03/mri/orig.mgz 
    18. 

  18. 

  19. #--------------------------------------------
    20. 

  20. #@# Talairach Wed Oct 16 15:51:39 UTC 2019
    21. 

  21. 

  22.  mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 
    23. 

  23. 

  24. 

  25.  talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm 
    26. 

  26. 

  27. talairach_avi log file is transforms/talairach_avi.log...
    28. 

  28. 

  29.  cp transforms/talairach.auto.xfm transforms/talairach.xfm 
    30. 

  30. 

  31. #--------------------------------------------
    32. 

  32. #@# Talairach Failure Detection Wed Oct 16 15:53:06 UTC 2019
    33. 

  33. 

  34.  talairach_afd -T 0.005 -xfm transforms/talairach.xfm 
    35. 

  35. 

  36. 

  37.  awk -f /opt/freesurfer/bin/extract_talairach_avi_QA.awk /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-03/mri/transforms/talairach_avi.log 
    38. 

  38. 

  39. 

  40.  tal_QC_AZS /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-03/mri/transforms/talairach_avi.log 
    41. 

  41. 

  42. #--------------------------------------------
    43. 

  43. #@# Nu Intensity Correction Wed Oct 16 15:53:06 UTC 2019
    44. 

  44. 

  45.  mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 
    46. 

  46. 

  47. 

  48.  mri_add_xform_to_header -c /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-03/mri/transforms/talairach.xfm nu.mgz nu.mgz 
    49. 

  49. 

  50. #--------------------------------------------
    51. 

  51. #@# Intensity Normalization Wed Oct 16 15:54:42 UTC 2019
    52. 

  52. 

  53.  mri_normalize -g 1 -mprage nu.mgz T1.mgz 
    54. 

  54. 

  55. 

  56. 

  57. #---------------------------------
    58. 

  58. # New invocation of recon-all Wed Oct 16 17:21:11 UTC 2019 
    59. 

  59. #-------------------------------------
    60. 

  60. #@# EM Registration Wed Oct 16 17:21:15 UTC 2019
    61. 

  61. 

  62.  mri_em_register -rusage /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-03/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta 
    63. 

  63. 

  64. #--------------------------------------
    65. 

  65. #@# CA Normalize Wed Oct 16 17:25:25 UTC 2019
    66. 

  66. 

  67.  mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta norm.mgz 
    68. 

  68. 

  69. #--------------------------------------
    70. 

  70. #@# CA Reg Wed Oct 16 17:26:35 UTC 2019
    71. 

  71. 

  72.  mri_ca_register -rusage /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-03/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.m3z 
    73. 

  73. 

  74. #--------------------------------------
    75. 

  75. #@# SubCort Seg Wed Oct 16 19:03:24 UTC 2019
    76. 

  76. 

  77.  mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz 
    78. 

  78. 

  79. 

  80.  mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-03/mri/transforms/cc_up.lta sub-03 
    81. 

  81. 

  82. #--------------------------------------
    83. 

  83. #@# Merge ASeg Wed Oct 16 19:35:07 UTC 2019
    84. 

  84. 

  85.  cp aseg.auto.mgz aseg.presurf.mgz 
    86. 

  86. 

  87. #--------------------------------------------
    88. 

  88. #@# Intensity Normalization2 Wed Oct 16 19:35:07 UTC 2019
    89. 

  89. 

  90.  mri_normalize -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz 
    91. 

  91. 

  92. #--------------------------------------------
    93. 

  93. #@# Mask BFS Wed Oct 16 19:37:04 UTC 2019
    94. 

  94. 

  95.  mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz 
    96. 

  96. 

  97. #--------------------------------------------
    98. 

  98. #@# WM Segmentation Wed Oct 16 19:37:07 UTC 2019
    99. 

  99. 

  100.  mri_segment -mprage brain.mgz wm.seg.mgz 
    101. 

  101. 

  102. 

  103.  mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz 
    104. 

  104. 

  105. 

  106.  mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz 
    107. 

  107. 

  108. #--------------------------------------------
    109. 

  109. #@# Fill Wed Oct 16 19:38:17 UTC 2019
    110. 

  110. 

  111.  mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz 
    112. 

  112. 

  113. 

  114. 

  115. #---------------------------------
    116. 

  116. # New invocation of recon-all Wed Oct 16 21:00:22 UTC 2019 
    117. 

  117. #--------------------------------------------
    118. 

  118. #@# Cortical ribbon mask Wed Oct 16 21:00:24 UTC 2019
    119. 

  119. 

  120.  mris_volmask --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon sub-03 
    121. 

  121. 

  122. #-----------------------------------------
    123. 

  123. #@# Parcellation Stats lh Wed Oct 16 21:05:07 UTC 2019
    124. 

  124. 

  125.  mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab sub-03 lh white 
    126. 

  126. 

  127. 

  128.  mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab sub-03 lh pial 
    129. 

  129. 

  130. #-----------------------------------------
    131. 

  131. #@# Cortical Parc 2 lh Wed Oct 16 21:05:47 UTC 2019
    132. 

  132. 

  133.  mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-03 lh ../surf/lh.sphere.reg /opt/freesurfer/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot 
    134. 

  134. 

  135. #-----------------------------------------
    136. 

  136. #@# Parcellation Stats 2 lh Wed Oct 16 21:05:58 UTC 2019
    137. 

  137. 

  138.  mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab sub-03 lh white 
    139. 

  139. 

  140. #-----------------------------------------
    141. 

  141. #@# Cortical Parc 3 lh Wed Oct 16 21:06:18 UTC 2019
    142. 

  142. 

  143.  mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-03 lh ../surf/lh.sphere.reg /opt/freesurfer/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot 
    144. 

  144. 

  145. #-----------------------------------------
    146. 

  146. #@# Parcellation Stats 3 lh Wed Oct 16 21:06:27 UTC 2019
    147. 

  147. 

  148.  mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab sub-03 lh white 
    149. 

  149. 

  150. #-----------------------------------------
    151. 

  151. #@# WM/GM Contrast lh Wed Oct 16 21:06:47 UTC 2019
    152. 

  152. 

  153.  pctsurfcon --s sub-03 --lh-only 
    154. 

  154. 

  155. #-----------------------------------------
    156. 

  156. #@# Relabel Hypointensities Wed Oct 16 21:06:52 UTC 2019
    157. 

  157. 

  158.  mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz 
    159. 

  159. 

  160. #-----------------------------------------
    161. 

  161. #@# AParc-to-ASeg aparc Wed Oct 16 21:07:05 UTC 2019
    162. 

  162. 

  163.  mri_aparc2aseg --s sub-03 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt 
    164. 

  164. 

  165. #-----------------------------------------
    166. 

  166. #@# AParc-to-ASeg a2009s Wed Oct 16 21:10:06 UTC 2019
    167. 

  167. INFO: skipping a2009s aparc2aseg
    168. 

  168. #-----------------------------------------
    169. 

  169. #@# AParc-to-ASeg DKTatlas Wed Oct 16 21:10:06 UTC 2019
    170. 

  170. INFO: skipping DKTatlas aparc2aseg
    171. 

  171. #-----------------------------------------
    172. 

  172. #@# APas-to-ASeg Wed Oct 16 21:10:06 UTC 2019
    173. 

  173. 

  174.  apas2aseg --i aparc+aseg.mgz --o aseg.mgz 
    175. 

  175. 

  176. #--------------------------------------------
    177. 

  177. #@# ASeg Stats Wed Oct 16 21:10:09 UTC 2019
    178. 

  178. 

  179.  mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /opt/freesurfer/ASegStatsLUT.txt --subject sub-03 
    180. 

  180. 

  181. #-----------------------------------------
    182. 

  182. #@# WMParc Wed Oct 16 21:10:33 UTC 2019
    183. 

  183. 

  184.  mri_aparc2aseg --s sub-03 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz 
    185. 

  185. 

  186. 

  187.  mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject sub-03 --surf-wm-vol --ctab /opt/freesurfer/WMParcStatsLUT.txt --etiv 
    188. 

  188. 

  189. #--------------------------------------------
    190. 

  190. #@# BA_exvivo Labels lh Wed Oct 16 21:13:58 UTC 2019
    191. 

  191. 

  192.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.BA1_exvivo.label --trgsubject sub-03 --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface 
    193. 

  193. 

  194. 

  195.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.BA2_exvivo.label --trgsubject sub-03 --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface 
    196. 

  196. 

  197. 

  198.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.BA3a_exvivo.label --trgsubject sub-03 --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface 
    199. 

  199. 

  200. 

  201.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.BA3b_exvivo.label --trgsubject sub-03 --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface 
    202. 

  202. 

  203. 

  204.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.BA4a_exvivo.label --trgsubject sub-03 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface 
    205. 

  205. 

  206. 

  207.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.BA4p_exvivo.label --trgsubject sub-03 --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface 
    208. 

  208. 

  209. 

  210.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.BA6_exvivo.label --trgsubject sub-03 --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface 
    211. 

  211. 

  212. 

  213.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.BA44_exvivo.label --trgsubject sub-03 --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface 
    214. 

  214. 

  215. 

  216.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.BA45_exvivo.label --trgsubject sub-03 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface 
    217. 

  217. 

  218. 

  219.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.V1_exvivo.label --trgsubject sub-03 --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface 
    220. 

  220. 

  221. 

  222.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.V2_exvivo.label --trgsubject sub-03 --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface 
    223. 

  223. 

  224. 

  225.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.MT_exvivo.label --trgsubject sub-03 --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface 
    226. 

  226. 

  227. 

  228.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject sub-03 --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface 
    229. 

  229. 

  230. 

  231.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject sub-03 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface 
    232. 

  232. 

  233. 

  234.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject sub-03 --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface 
    235. 

  235. 

  236. 

  237.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject sub-03 --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface 
    238. 

  238. 

  239. 

  240.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject sub-03 --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface 
    241. 

  241. 

  242. 

  243.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject sub-03 --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface 
    244. 

  244. 

  245. 

  246.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject sub-03 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface 
    247. 

  247. 

  248. 

  249.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject sub-03 --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface 
    250. 

  250. 

  251. 

  252.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject sub-03 --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface 
    253. 

  253. 

  254. 

  255.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject sub-03 --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface 
    256. 

  256. 

  257. 

  258.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject sub-03 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface 
    259. 

  259. 

  260. 

  261.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject sub-03 --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface 
    262. 

  262. 

  263. 

  264.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject sub-03 --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface 
    265. 

  265. 

  266. 

  267.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject sub-03 --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface 
    268. 

  268. 

  269. 

  270.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject sub-03 --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface 
    271. 

  271. 

  272. 

  273.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject sub-03 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface 
    274. 

  274. 

  275. 

  276.  mris_label2annot --s sub-03 --hemi lh --ctab /opt/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.entorhinal_exvivo.label --l lh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose 
    277. 

  277. 

  278. 

  279.  mris_label2annot --s sub-03 --hemi lh --ctab /opt/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose 
    280. 

  280. 

  281. 

  282.  mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.stats -b -a ./lh.BA_exvivo.annot -c ./BA_exvivo.ctab sub-03 lh white 
    283. 

  283. 

  284. 

  285.  mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab sub-03 lh white 
    286. 

  286. 

  287. 

  288. 

  289. #---------------------------------
    290. 

  290. # New invocation of recon-all Wed Oct 16 21:17:13 UTC 2019 
    291. 

  291. #-----------------------------------------
    292. 

  292. #@# Parcellation Stats rh Wed Oct 16 21:17:14 UTC 2019
    293. 

  293. 

  294.  mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab sub-03 rh white 
    295. 

  295. 

  296. 

  297.  mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab sub-03 rh pial 
    298. 

  298. 

  299. #-----------------------------------------
    300. 

  300. #@# Cortical Parc 2 rh Wed Oct 16 21:17:54 UTC 2019
    301. 

  301. 

  302.  mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-03 rh ../surf/rh.sphere.reg /opt/freesurfer/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot 
    303. 

  303. 

  304. #-----------------------------------------
    305. 

  305. #@# Parcellation Stats 2 rh Wed Oct 16 21:18:05 UTC 2019
    306. 

  306. 

  307.  mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab sub-03 rh white 
    308. 

  308. 

  309. #-----------------------------------------
    310. 

  310. #@# Cortical Parc 3 rh Wed Oct 16 21:18:25 UTC 2019
    311. 

  311. 

  312.  mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-03 rh ../surf/rh.sphere.reg /opt/freesurfer/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.DKTatlas.annot 
    313. 

  313. 

  314. #-----------------------------------------
    315. 

  315. #@# Parcellation Stats 3 rh Wed Oct 16 21:18:33 UTC 2019
    316. 

  316. 

  317.  mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab sub-03 rh white 
    318. 

  318. 

  319. #-----------------------------------------
    320. 

  320. #@# WM/GM Contrast rh Wed Oct 16 21:18:53 UTC 2019
    321. 

  321. 

  322.  pctsurfcon --s sub-03 --rh-only 
    323. 

  323. 

  324. #-----------------------------------------
    325. 

  325. #@# AParc-to-ASeg aparc Wed Oct 16 21:18:58 UTC 2019
    326. 

  326. 

  327.  mri_aparc2aseg --s sub-03 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt 
    328. 

  328. 

  329. #-----------------------------------------
    330. 

  330. #@# AParc-to-ASeg a2009s Wed Oct 16 21:21:55 UTC 2019
    331. 

  331. 

  332.  mri_aparc2aseg --s sub-03 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --a2009s 
    333. 

  333. 

  334. #-----------------------------------------
    335. 

  335. #@# AParc-to-ASeg DKTatlas Wed Oct 16 21:24:52 UTC 2019
    336. 

  336. 

  337.  mri_aparc2aseg --s sub-03 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --annot aparc.DKTatlas --o mri/aparc.DKTatlas+aseg.mgz 
    338. 

  338. 

  339. #--------------------------------------------
    340. 

  340. #@# BA_exvivo Labels rh Wed Oct 16 21:27:53 UTC 2019
    341. 

  341. 

  342.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.BA1_exvivo.label --trgsubject sub-03 --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface 
    343. 

  343. 

  344. 

  345.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.BA2_exvivo.label --trgsubject sub-03 --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface 
    346. 

  346. 

  347. 

  348.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.BA3a_exvivo.label --trgsubject sub-03 --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface 
    349. 

  349. 

  350. 

  351.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.BA3b_exvivo.label --trgsubject sub-03 --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface 
    352. 

  352. 

  353. 

  354.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.BA4a_exvivo.label --trgsubject sub-03 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface 
    355. 

  355. 

  356. 

  357.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.BA4p_exvivo.label --trgsubject sub-03 --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface 
    358. 

  358. 

  359. 

  360.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.BA6_exvivo.label --trgsubject sub-03 --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface 
    361. 

  361. 

  362. 

  363.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.BA44_exvivo.label --trgsubject sub-03 --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface 
    364. 

  364. 

  365. 

  366.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.BA45_exvivo.label --trgsubject sub-03 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface 
    367. 

  367. 

  368. 

  369.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.V1_exvivo.label --trgsubject sub-03 --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface 
    370. 

  370. 

  371. 

  372.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.V2_exvivo.label --trgsubject sub-03 --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface 
    373. 

  373. 

  374. 

  375.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.MT_exvivo.label --trgsubject sub-03 --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface 
    376. 

  376. 

  377. 

  378.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject sub-03 --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface 
    379. 

  379. 

  380. 

  381.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject sub-03 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface 
    382. 

  382. 

  383. 

  384.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject sub-03 --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface 
    385. 

  385. 

  386. 

  387.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject sub-03 --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface 
    388. 

  388. 

  389. 

  390.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject sub-03 --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface 
    391. 

  391. 

  392. 

  393.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject sub-03 --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface 
    394. 

  394. 

  395. 

  396.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject sub-03 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface 
    397. 

  397. 

  398. 

  399.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject sub-03 --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface 
    400. 

  400. 

  401. 

  402.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject sub-03 --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface 
    403. 

  403. 

  404. 

  405.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject sub-03 --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface 
    406. 

  406. 

  407. 

  408.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject sub-03 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface 
    409. 

  409. 

  410. 

  411.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject sub-03 --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface 
    412. 

  412. 

  413. 

  414.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject sub-03 --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface 
    415. 

  415. 

  416. 

  417.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject sub-03 --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface 
    418. 

  418. 

  419. 

  420.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject sub-03 --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface 
    421. 

  421. 

  422. 

  423.  mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject sub-03 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface 
    424. 

  424. 

  425. 

  426.  mris_label2annot --s sub-03 --hemi rh --ctab /opt/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.entorhinal_exvivo.label --l rh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose 
    427. 

  427. 

  428. 

  429.  mris_label2annot --s sub-03 --hemi rh --ctab /opt/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose 
    430. 

  430. 

  431. 

  432.  mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.stats -b -a ./rh.BA_exvivo.annot -c ./BA_exvivo.ctab sub-03 rh white 
    433. 

  433. 

  434. 

  435.  mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab sub-03 rh white 
    436. 

  436. 

  437. 

  438. 

  439. #---------------------------------
    440. 

  440. # New invocation of recon-all Wed Oct 16 21:31:10 UTC 2019 
    441. 

  441. #-----------------------------------------
    442. 

  442. #@# APas-to-ASeg Wed Oct 16 21:31:11 UTC 2019
    443. 

  443. 

  444.  apas2aseg --i aparc+aseg.mgz --o aseg.mgz 
    445. 

  445.