mri_convert /data/in/sub-02/anat/sub-02_T1w.nii.gz /data/out/sub-02/mri/orig/001.mgz #-------------------------------------------- #@# MotionCor Sat Jan 14 08:35:59 UTC 2017 cp /data/out/sub-02/mri/orig/001.mgz /data/out/sub-02/mri/rawavg.mgz mri_convert /data/out/sub-02/mri/rawavg.mgz /data/out/sub-02/mri/orig.mgz --conform mri_add_xform_to_header -c /data/out/sub-02/mri/transforms/talairach.xfm /data/out/sub-02/mri/orig.mgz /data/out/sub-02/mri/orig.mgz #-------------------------------------------- #@# Talairach Sat Jan 14 08:36:08 UTC 2017 mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Sat Jan 14 08:37:15 UTC 2017 talairach_afd -T 0.005 -xfm transforms/talairach.xfm awk -f /opt/freesurfer/bin/extract_talairach_avi_QA.awk /data/out/sub-02/mri/transforms/talairach_avi.log tal_QC_AZS /data/out/sub-02/mri/transforms/talairach_avi.log #-------------------------------------------- #@# Nu Intensity Correction Sat Jan 14 08:37:16 UTC 2017 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 mri_add_xform_to_header -c /data/out/sub-02/mri/transforms/talairach.xfm nu.mgz nu.mgz #-------------------------------------------- #@# Intensity Normalization Sat Jan 14 08:38:18 UTC 2017 mri_normalize -g 1 nu.mgz T1.mgz #-------------------------------------------- #@# Skull Stripping Sat Jan 14 08:39:56 UTC 2017 mri_em_register -skull nu.mgz /opt/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta mri_watershed -T1 -brain_atlas /opt/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Sat Jan 14 09:04:38 UTC 2017 mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /opt/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta #-------------------------------------- #@# CA Normalize Sat Jan 14 09:23:36 UTC 2017 mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /opt/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz #-------------------------------------- #@# CA Reg Sat Jan 14 09:24:59 UTC 2017 mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /opt/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.m3z #-------------------------------------- #@# CA Reg Inv Sat Jan 14 11:57:34 UTC 2017 mri_ca_register -invert-and-save transforms/talairach.m3z #-------------------------------------- #@# Remove Neck Sat Jan 14 11:58:33 UTC 2017 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /opt/freesurfer/average/RB_all_2008-03-26.gca nu_noneck.mgz #-------------------------------------- #@# SkullLTA Sat Jan 14 11:59:36 UTC 2017 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /opt/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta #-------------------------------------- #@# SubCort Seg Sat Jan 14 12:20:20 UTC 2017 mri_ca_label -align norm.mgz transforms/talairach.m3z /opt/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /data/out/sub-02/mri/transforms/cc_up.lta sub-02 #-------------------------------------- #@# Merge ASeg Sat Jan 14 12:37:57 UTC 2017 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Sat Jan 14 12:37:57 UTC 2017 mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz #-------------------------------------------- #@# Mask BFS Sat Jan 14 12:40:46 UTC 2017 mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz #-------------------------------------------- #@# WM Segmentation Sat Jan 14 12:40:48 UTC 2017 mri_segment brain.mgz wm.seg.mgz mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz #-------------------------------------------- #@# Fill Sat Jan 14 12:42:25 UTC 2017 mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz #-------------------------------------------- #@# Tessellate lh Sat Jan 14 12:43:03 UTC 2017 mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix #-------------------------------------------- #@# Smooth1 lh Sat Jan 14 12:43:08 UTC 2017 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix #-------------------------------------------- #@# Inflation1 lh Sat Jan 14 12:43:10 UTC 2017 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix #-------------------------------------------- #@# QSphere lh Sat Jan 14 12:43:30 UTC 2017 mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix #-------------------------------------------- #@# Fix Topology lh Sat Jan 14 12:46:21 UTC 2017 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub-02 lh mris_euler_number ../surf/lh.orig mris_remove_intersection ../surf/lh.orig ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Sat Jan 14 12:59:01 UTC 2017 mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub-02 lh #-------------------------------------------- #@# Smooth2 lh Sat Jan 14 13:02:29 UTC 2017 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm #-------------------------------------------- #@# Inflation2 lh Sat Jan 14 13:02:32 UTC 2017 mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated #----------------------------------------- #@# Curvature Stats lh Sat Jan 14 13:03:48 UTC 2017 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub-02 lh curv sulc #-------------------------------------------- #@# Sphere lh Sat Jan 14 13:03:51 UTC 2017 mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere #-------------------------------------------- #@# Surf Reg lh Sat Jan 14 13:30:11 UTC 2017 mris_register -curv ../surf/lh.sphere /opt/freesurfer/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg #-------------------------------------------- #@# Jacobian white lh Sat Jan 14 13:44:00 UTC 2017 mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Sat Jan 14 13:44:02 UTC 2017 mrisp_paint -a 5 /opt/freesurfer/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv #----------------------------------------- #@# Cortical Parc lh Sat Jan 14 13:44:03 UTC 2017 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub-02 lh ../surf/lh.sphere.reg /opt/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot #-------------------------------------------- #@# Make Pial Surf lh Sat Jan 14 13:44:33 UTC 2017 mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub-02 lh #-------------------------------------------- #@# Surf Volume lh Sat Jan 14 13:51:02 UTC 2017 mris_calc -o lh.area.mid lh.area add lh.area.pial mris_calc -o lh.area.mid lh.area.mid div 2 mris_calc -o lh.volume lh.area.mid mul lh.thickness #----------------------------------------- #@# WM/GM Contrast lh Sat Jan 14 13:51:03 UTC 2017 pctsurfcon --s sub-02 --lh-only #----------------------------------------- #@# Parcellation Stats lh Sat Jan 14 13:51:07 UTC 2017 mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab sub-02 lh white #----------------------------------------- #@# Cortical Parc 2 lh Sat Jan 14 13:51:15 UTC 2017 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub-02 lh ../surf/lh.sphere.reg /opt/freesurfer/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot #----------------------------------------- #@# Parcellation Stats 2 lh Sat Jan 14 13:51:53 UTC 2017 mris_anatomical_stats -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-02 lh white #----------------------------------------- #@# Cortical Parc 3 lh Sat Jan 14 13:52:01 UTC 2017 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub-02 lh ../surf/lh.sphere.reg /opt/freesurfer/average/lh.DKTatlas40.gcs ../label/lh.aparc.DKTatlas40.annot #----------------------------------------- #@# Parcellation Stats 3 lh Sat Jan 14 13:52:30 UTC 2017 mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab sub-02 lh white #-------------------------------------------- #@# Tessellate rh Sat Jan 14 13:52:38 UTC 2017 mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix #-------------------------------------------- #@# Smooth1 rh Sat Jan 14 13:52:42 UTC 2017 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix #-------------------------------------------- #@# Inflation1 rh Sat Jan 14 13:52:45 UTC 2017 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix #-------------------------------------------- #@# QSphere rh Sat Jan 14 13:53:04 UTC 2017 mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix #-------------------------------------------- #@# Fix Topology rh Sat Jan 14 13:55:27 UTC 2017 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub-02 rh mris_euler_number ../surf/rh.orig mris_remove_intersection ../surf/rh.orig ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Sat Jan 14 14:09:18 UTC 2017 mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub-02 rh #-------------------------------------------- #@# Smooth2 rh Sat Jan 14 14:12:18 UTC 2017 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm #-------------------------------------------- #@# Inflation2 rh Sat Jan 14 14:12:20 UTC 2017 mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated #----------------------------------------- #@# Curvature Stats rh Sat Jan 14 14:13:26 UTC 2017 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub-02 rh curv sulc #-------------------------------------------- #@# Sphere rh Sat Jan 14 14:13:29 UTC 2017 mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere #-------------------------------------------- #@# Surf Reg rh Sat Jan 14 14:28:17 UTC 2017 mris_register -curv ../surf/rh.sphere /opt/freesurfer/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg #-------------------------------------------- #@# Jacobian white rh Sat Jan 14 14:41:19 UTC 2017 mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv rh Sat Jan 14 14:41:21 UTC 2017 mrisp_paint -a 5 /opt/freesurfer/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv #----------------------------------------- #@# Cortical Parc rh Sat Jan 14 14:41:22 UTC 2017 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub-02 rh ../surf/rh.sphere.reg /opt/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot #-------------------------------------------- #@# Make Pial Surf rh Sat Jan 14 14:41:51 UTC 2017 mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub-02 rh #-------------------------------------------- #@# Surf Volume rh Sat Jan 14 14:47:58 UTC 2017 mris_calc -o rh.area.mid rh.area add rh.area.pial mris_calc -o rh.area.mid rh.area.mid div 2 mris_calc -o rh.volume rh.area.mid mul rh.thickness #----------------------------------------- #@# WM/GM Contrast rh Sat Jan 14 14:47:59 UTC 2017 pctsurfcon --s sub-02 --rh-only #----------------------------------------- #@# Parcellation Stats rh Sat Jan 14 14:48:03 UTC 2017 mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab sub-02 rh white #----------------------------------------- #@# Cortical Parc 2 rh Sat Jan 14 14:48:10 UTC 2017 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub-02 rh ../surf/rh.sphere.reg /opt/freesurfer/average/rh.destrieux.simple.2009-07-29.gcs ../label/rh.aparc.a2009s.annot #----------------------------------------- #@# Parcellation Stats 2 rh Sat Jan 14 14:48:47 UTC 2017 mris_anatomical_stats -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-02 rh white #----------------------------------------- #@# Cortical Parc 3 rh Sat Jan 14 14:48:55 UTC 2017 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub-02 rh ../surf/rh.sphere.reg /opt/freesurfer/average/rh.DKTatlas40.gcs ../label/rh.aparc.DKTatlas40.annot #----------------------------------------- #@# Parcellation Stats 3 rh Sat Jan 14 14:49:24 UTC 2017 mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas40.stats -b -a ../label/rh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab sub-02 rh white #-------------------------------------------- #@# Cortical ribbon mask Sat Jan 14 14:49:31 UTC 2017 mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon sub-02 #-------------------------------------------- #@# ASeg Stats Sat Jan 14 14:54:33 UTC 2017 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-02 #----------------------------------------- #@# AParc-to-ASeg Sat Jan 14 14:56:30 UTC 2017 mri_aparc2aseg --s sub-02 --volmask mri_aparc2aseg --s sub-02 --volmask --a2009s #----------------------------------------- #@# WMParc Sat Jan 14 14:57:52 UTC 2017 mri_aparc2aseg --s sub-02 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz 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-02 --surf-wm-vol --ctab /opt/freesurfer/WMParcStatsLUT.txt --etiv #-------------------------------------------- #@# BA Labels lh Sat Jan 14 15:04:52 UTC 2017 mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA1.label --trgsubject sub-02 --trglabel ./lh.BA1.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA2.label --trgsubject sub-02 --trglabel ./lh.BA2.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA3a.label --trgsubject sub-02 --trglabel ./lh.BA3a.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA3b.label --trgsubject sub-02 --trglabel ./lh.BA3b.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA4a.label --trgsubject sub-02 --trglabel ./lh.BA4a.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA4p.label --trgsubject sub-02 --trglabel ./lh.BA4p.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA6.label --trgsubject sub-02 --trglabel ./lh.BA6.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA44.label --trgsubject sub-02 --trglabel ./lh.BA44.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA45.label --trgsubject sub-02 --trglabel ./lh.BA45.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.V1.label --trgsubject sub-02 --trglabel ./lh.V1.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.V2.label --trgsubject sub-02 --trglabel ./lh.V2.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.MT.label --trgsubject sub-02 --trglabel ./lh.MT.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.perirhinal.label --trgsubject sub-02 --trglabel ./lh.perirhinal.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA1.thresh.label --trgsubject sub-02 --trglabel ./lh.BA1.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA2.thresh.label --trgsubject sub-02 --trglabel ./lh.BA2.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA3a.thresh.label --trgsubject sub-02 --trglabel ./lh.BA3a.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA3b.thresh.label --trgsubject sub-02 --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA4a.thresh.label --trgsubject sub-02 --trglabel ./lh.BA4a.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA4p.thresh.label --trgsubject sub-02 --trglabel ./lh.BA4p.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA6.thresh.label --trgsubject sub-02 --trglabel ./lh.BA6.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA44.thresh.label --trgsubject sub-02 --trglabel ./lh.BA44.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA45.thresh.label --trgsubject sub-02 --trglabel ./lh.BA45.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.V1.thresh.label --trgsubject sub-02 --trglabel ./lh.V1.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.V2.thresh.label --trgsubject sub-02 --trglabel ./lh.V2.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.MT.thresh.label --trgsubject sub-02 --trglabel ./lh.MT.thresh.label --hemi lh --regmethod surface mris_label2annot --s sub-02 --hemi lh --ctab /opt/freesurfer/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --l lh.perirhinal.label --a BA --maxstatwinner --noverbose mris_label2annot --s sub-02 --hemi lh --ctab /opt/freesurfer/average/colortable_BA.txt --l lh.BA1.thresh.label --l lh.BA2.thresh.label --l lh.BA3a.thresh.label --l lh.BA3b.thresh.label --l lh.BA4a.thresh.label --l lh.BA4p.thresh.label --l lh.BA6.thresh.label --l lh.BA44.thresh.label --l lh.BA45.thresh.label --l lh.V1.thresh.label --l lh.V2.thresh.label --l lh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab sub-02 lh white mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab sub-02 lh white #-------------------------------------------- #@# BA Labels rh Sat Jan 14 15:07:16 UTC 2017 mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA1.label --trgsubject sub-02 --trglabel ./rh.BA1.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA2.label --trgsubject sub-02 --trglabel ./rh.BA2.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA3a.label --trgsubject sub-02 --trglabel ./rh.BA3a.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA3b.label --trgsubject sub-02 --trglabel ./rh.BA3b.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA4a.label --trgsubject sub-02 --trglabel ./rh.BA4a.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA4p.label --trgsubject sub-02 --trglabel ./rh.BA4p.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA6.label --trgsubject sub-02 --trglabel ./rh.BA6.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA44.label --trgsubject sub-02 --trglabel ./rh.BA44.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA45.label --trgsubject sub-02 --trglabel ./rh.BA45.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.V1.label --trgsubject sub-02 --trglabel ./rh.V1.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.V2.label --trgsubject sub-02 --trglabel ./rh.V2.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.MT.label --trgsubject sub-02 --trglabel ./rh.MT.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.perirhinal.label --trgsubject sub-02 --trglabel ./rh.perirhinal.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA1.thresh.label --trgsubject sub-02 --trglabel ./rh.BA1.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA2.thresh.label --trgsubject sub-02 --trglabel ./rh.BA2.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA3a.thresh.label --trgsubject sub-02 --trglabel ./rh.BA3a.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA3b.thresh.label --trgsubject sub-02 --trglabel ./rh.BA3b.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA4a.thresh.label --trgsubject sub-02 --trglabel ./rh.BA4a.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA4p.thresh.label --trgsubject sub-02 --trglabel ./rh.BA4p.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA6.thresh.label --trgsubject sub-02 --trglabel ./rh.BA6.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA44.thresh.label --trgsubject sub-02 --trglabel ./rh.BA44.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA45.thresh.label --trgsubject sub-02 --trglabel ./rh.BA45.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.V1.thresh.label --trgsubject sub-02 --trglabel ./rh.V1.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.V2.thresh.label --trgsubject sub-02 --trglabel ./rh.V2.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.MT.thresh.label --trgsubject sub-02 --trglabel ./rh.MT.thresh.label --hemi rh --regmethod surface mris_label2annot --s sub-02 --hemi rh --ctab /opt/freesurfer/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --l rh.perirhinal.label --a BA --maxstatwinner --noverbose mris_label2annot --s sub-02 --hemi rh --ctab /opt/freesurfer/average/colortable_BA.txt --l rh.BA1.thresh.label --l rh.BA2.thresh.label --l rh.BA3a.thresh.label --l rh.BA3b.thresh.label --l rh.BA4a.thresh.label --l rh.BA4p.thresh.label --l rh.BA6.thresh.label --l rh.BA44.thresh.label --l rh.BA45.thresh.label --l rh.V1.thresh.label --l rh.V2.thresh.label --l rh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab sub-02 rh white mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab sub-02 rh white #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label lh Sat Jan 14 15:09:37 UTC 2017 mris_spherical_average -erode 1 -orig white -t 0.4 -o sub-02 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label sub-02 lh white #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label rh Sat Jan 14 15:09:47 UTC 2017 mris_spherical_average -erode 1 -orig white -t 0.4 -o sub-02 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label sub-02 rh white