recon-all.cmd 30 KB

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  1. #---------------------------------
  2. # New invocation of recon-all Wed Oct 16 15:51:15 UTC 2019
  3. mri_convert /scratch/03763/oesteban/fmriprep-work/sub-05/fmriprep_wf/single_subject_05_wf/anat_preproc_wf/anat_validate/sub-05_ses-retest_T1w_template_valid.nii.gz /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-05/mri/orig/001.mgz
  4. #--------------------------------------------
  5. #@# MotionCor Wed Oct 16 15:51:29 UTC 2019
  6. cp /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-05/mri/orig/001.mgz /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-05/mri/rawavg.mgz
  7. mri_convert /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-05/mri/rawavg.mgz /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-05/mri/orig.mgz --conform
  8. mri_add_xform_to_header -c /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-05/mri/transforms/talairach.xfm /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-05/mri/orig.mgz /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-05/mri/orig.mgz
  9. #--------------------------------------------
  10. #@# Talairach Wed Oct 16 15:51:39 UTC 2019
  11. mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
  12. talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
  13. talairach_avi log file is transforms/talairach_avi.log...
  14. cp transforms/talairach.auto.xfm transforms/talairach.xfm
  15. #--------------------------------------------
  16. #@# Talairach Failure Detection Wed Oct 16 15:53:03 UTC 2019
  17. talairach_afd -T 0.005 -xfm transforms/talairach.xfm
  18. awk -f /opt/freesurfer/bin/extract_talairach_avi_QA.awk /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-05/mri/transforms/talairach_avi.log
  19. tal_QC_AZS /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-05/mri/transforms/talairach_avi.log
  20. #--------------------------------------------
  21. #@# Nu Intensity Correction Wed Oct 16 15:53:03 UTC 2019
  22. mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
  23. mri_add_xform_to_header -c /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-05/mri/transforms/talairach.xfm nu.mgz nu.mgz
  24. #--------------------------------------------
  25. #@# Intensity Normalization Wed Oct 16 15:54:40 UTC 2019
  26. mri_normalize -g 1 -mprage nu.mgz T1.mgz
  27. #---------------------------------
  28. # New invocation of recon-all Wed Oct 16 17:21:27 UTC 2019
  29. #-------------------------------------
  30. #@# EM Registration Wed Oct 16 17:21:32 UTC 2019
  31. mri_em_register -rusage /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-05/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
  32. #--------------------------------------
  33. #@# CA Normalize Wed Oct 16 17:24:35 UTC 2019
  34. 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
  35. #--------------------------------------
  36. #@# CA Reg Wed Oct 16 17:25:45 UTC 2019
  37. mri_ca_register -rusage /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-05/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
  38. #--------------------------------------
  39. #@# SubCort Seg Wed Oct 16 18:45:06 UTC 2019
  40. 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
  41. 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-05/mri/transforms/cc_up.lta sub-05
  42. #--------------------------------------
  43. #@# Merge ASeg Wed Oct 16 19:23:08 UTC 2019
  44. cp aseg.auto.mgz aseg.presurf.mgz
  45. #--------------------------------------------
  46. #@# Intensity Normalization2 Wed Oct 16 19:23:08 UTC 2019
  47. mri_normalize -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz
  48. #--------------------------------------------
  49. #@# Mask BFS Wed Oct 16 19:25:04 UTC 2019
  50. mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
  51. #--------------------------------------------
  52. #@# WM Segmentation Wed Oct 16 19:25:06 UTC 2019
  53. mri_segment -mprage brain.mgz wm.seg.mgz
  54. mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz
  55. mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz
  56. #--------------------------------------------
  57. #@# Fill Wed Oct 16 19:26:19 UTC 2019
  58. mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz
  59. #---------------------------------
  60. # New invocation of recon-all Wed Oct 16 21:14:41 UTC 2019
  61. #--------------------------------------------
  62. #@# Cortical ribbon mask Wed Oct 16 21:14:41 UTC 2019
  63. 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-05
  64. #-----------------------------------------
  65. #@# Parcellation Stats lh Wed Oct 16 21:21:37 UTC 2019
  66. 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-05 lh white
  67. 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-05 lh pial
  68. #-----------------------------------------
  69. #@# Cortical Parc 2 lh Wed Oct 16 21:22:27 UTC 2019
  70. mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-05 lh ../surf/lh.sphere.reg /opt/freesurfer/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot
  71. #-----------------------------------------
  72. #@# Parcellation Stats 2 lh Wed Oct 16 21:22:40 UTC 2019
  73. 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-05 lh white
  74. #-----------------------------------------
  75. #@# Cortical Parc 3 lh Wed Oct 16 21:23:05 UTC 2019
  76. mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-05 lh ../surf/lh.sphere.reg /opt/freesurfer/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot
  77. #-----------------------------------------
  78. #@# Parcellation Stats 3 lh Wed Oct 16 21:23:16 UTC 2019
  79. 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-05 lh white
  80. #-----------------------------------------
  81. #@# WM/GM Contrast lh Wed Oct 16 21:23:41 UTC 2019
  82. pctsurfcon --s sub-05 --lh-only
  83. #-----------------------------------------
  84. #@# Relabel Hypointensities Wed Oct 16 21:23:47 UTC 2019
  85. mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz
  86. #-----------------------------------------
  87. #@# AParc-to-ASeg aparc Wed Oct 16 21:24:01 UTC 2019
  88. mri_aparc2aseg --s sub-05 --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
  89. #-----------------------------------------
  90. #@# AParc-to-ASeg a2009s Wed Oct 16 21:27:13 UTC 2019
  91. INFO: skipping a2009s aparc2aseg
  92. #-----------------------------------------
  93. #@# AParc-to-ASeg DKTatlas Wed Oct 16 21:27:13 UTC 2019
  94. INFO: skipping DKTatlas aparc2aseg
  95. #-----------------------------------------
  96. #@# APas-to-ASeg Wed Oct 16 21:27:13 UTC 2019
  97. apas2aseg --i aparc+aseg.mgz --o aseg.mgz
  98. #--------------------------------------------
  99. #@# ASeg Stats Wed Oct 16 21:27:16 UTC 2019
  100. 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-05
  101. #-----------------------------------------
  102. #@# WMParc Wed Oct 16 21:27:42 UTC 2019
  103. mri_aparc2aseg --s sub-05 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz
  104. 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-05 --surf-wm-vol --ctab /opt/freesurfer/WMParcStatsLUT.txt --etiv
  105. #--------------------------------------------
  106. #@# BA_exvivo Labels lh Wed Oct 16 21:31:33 UTC 2019
  107. 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-05 --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface
  108. 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-05 --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface
  109. 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-05 --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface
  110. 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-05 --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface
  111. 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-05 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface
  112. 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-05 --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface
  113. 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-05 --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface
  114. 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-05 --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface
  115. 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-05 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface
  116. 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-05 --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface
  117. 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-05 --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface
  118. 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-05 --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface
  119. 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-05 --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface
  120. 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-05 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface
  121. 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-05 --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface
  122. 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-05 --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface
  123. 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-05 --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface
  124. 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-05 --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface
  125. 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-05 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface
  126. 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-05 --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface
  127. 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-05 --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface
  128. 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-05 --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface
  129. 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-05 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface
  130. 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-05 --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface
  131. 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-05 --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface
  132. 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-05 --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface
  133. 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-05 --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface
  134. 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-05 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface
  135. mris_label2annot --s sub-05 --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
  136. mris_label2annot --s sub-05 --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
  137. mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.stats -b -a ./lh.BA_exvivo.annot -c ./BA_exvivo.ctab sub-05 lh white
  138. 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-05 lh white
  139. #---------------------------------
  140. # New invocation of recon-all Wed Oct 16 21:35:20 UTC 2019
  141. #-----------------------------------------
  142. #@# Parcellation Stats rh Wed Oct 16 21:35:21 UTC 2019
  143. 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-05 rh white
  144. 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-05 rh pial
  145. #-----------------------------------------
  146. #@# Cortical Parc 2 rh Wed Oct 16 21:36:09 UTC 2019
  147. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-05 rh ../surf/rh.sphere.reg /opt/freesurfer/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot
  148. #-----------------------------------------
  149. #@# Parcellation Stats 2 rh Wed Oct 16 21:36:22 UTC 2019
  150. 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-05 rh white
  151. #-----------------------------------------
  152. #@# Cortical Parc 3 rh Wed Oct 16 21:36:46 UTC 2019
  153. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-05 rh ../surf/rh.sphere.reg /opt/freesurfer/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.DKTatlas.annot
  154. #-----------------------------------------
  155. #@# Parcellation Stats 3 rh Wed Oct 16 21:36:56 UTC 2019
  156. 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-05 rh white
  157. #-----------------------------------------
  158. #@# WM/GM Contrast rh Wed Oct 16 21:37:20 UTC 2019
  159. pctsurfcon --s sub-05 --rh-only
  160. #-----------------------------------------
  161. #@# AParc-to-ASeg aparc Wed Oct 16 21:37:26 UTC 2019
  162. mri_aparc2aseg --s sub-05 --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
  163. #-----------------------------------------
  164. #@# AParc-to-ASeg a2009s Wed Oct 16 21:40:37 UTC 2019
  165. mri_aparc2aseg --s sub-05 --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
  166. #-----------------------------------------
  167. #@# AParc-to-ASeg DKTatlas Wed Oct 16 21:43:49 UTC 2019
  168. mri_aparc2aseg --s sub-05 --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
  169. #--------------------------------------------
  170. #@# BA_exvivo Labels rh Wed Oct 16 21:46:59 UTC 2019
  171. 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-05 --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface
  172. 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-05 --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface
  173. 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-05 --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface
  174. 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-05 --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface
  175. 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-05 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface
  176. 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-05 --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface
  177. 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-05 --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface
  178. 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-05 --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface
  179. 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-05 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface
  180. 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-05 --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface
  181. 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-05 --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface
  182. 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-05 --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface
  183. 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-05 --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface
  184. 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-05 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface
  185. 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-05 --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface
  186. 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-05 --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface
  187. 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-05 --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface
  188. 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-05 --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface
  189. 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-05 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface
  190. 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-05 --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface
  191. 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-05 --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface
  192. 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-05 --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface
  193. 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-05 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface
  194. 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-05 --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface
  195. 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-05 --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface
  196. 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-05 --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface
  197. 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-05 --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface
  198. 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-05 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface
  199. mris_label2annot --s sub-05 --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
  200. mris_label2annot --s sub-05 --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
  201. mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.stats -b -a ./rh.BA_exvivo.annot -c ./BA_exvivo.ctab sub-05 rh white
  202. 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-05 rh white
  203. #---------------------------------
  204. # New invocation of recon-all Wed Oct 16 21:50:43 UTC 2019
  205. #-----------------------------------------
  206. #@# APas-to-ASeg Wed Oct 16 21:50:44 UTC 2019
  207. apas2aseg --i aparc+aseg.mgz --o aseg.mgz
  208. #---------------------------------
  209. # New invocation of recon-all Sat Jul 25 00:19:43 PDT 2020
  210. #-----------------------------------------
  211. #@# APas-to-ASeg Sat Jul 25 00:19:44 PDT 2020
  212. apas2aseg --i aparc+aseg.mgz --o aseg.mgz
  213. #---------------------------------
  214. # New invocation of recon-all Mon Jul 27 02:28:53 PDT 2020
  215. #-----------------------------------------
  216. #@# APas-to-ASeg Mon Jul 27 02:29:08 PDT 2020
  217. apas2aseg --i aparc+aseg.mgz --o aseg.mgz