mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub002/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig/001.mgz #-------------------------------------------- #@# T2/FLAIR Input Thu Aug 8 10:54:17 CEST 2013 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub002/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig/T2raw.mgz #-------------------------------------------- #@# MotionCor Thu Aug 8 10:54:34 CEST 2013 cp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig/001.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/rawavg.mgz mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig.mgz --conform --cw256 mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/talairach.xfm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig.mgz #-------------------------------------------- #@# Talairach Thu Aug 8 10:55:15 CEST 2013 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 Thu Aug 8 10:58:20 CEST 2013 talairach_afd -T 0.005 -xfm transforms/talairach.xfm awk -f /opt/freesurfer/5.3.0/bin/extract_talairach_avi_QA.awk /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/talairach_avi.log tal_QC_AZS /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/talairach_avi.log #-------------------------------------------- #@# Nu Intensity Correction Thu Aug 8 10:58:20 CEST 2013 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/talairach.xfm nu.mgz nu.mgz #-------------------------------------------- #@# Intensity Normalization Thu Aug 8 11:00:39 CEST 2013 mri_normalize -g 1 nu.mgz T1.mgz #-------------------------------------------- #@# Skull Stripping Thu Aug 8 11:03:30 CEST 2013 mri_em_register -skull nu.mgz /opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta mri_watershed -T1 -brain_atlas /opt/freesurfer/5.3.0/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 Thu Aug 8 11:38:34 CEST 2013 mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca transforms/talairach.lta #-------------------------------------- #@# CA Normalize Thu Aug 8 12:03:13 CEST 2013 mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz #-------------------------------------- #@# CA Reg Thu Aug 8 12:05:17 CEST 2013 mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca transforms/talairach.m3z #-------------------------------------- #@# CA Reg Inv Thu Aug 8 16:34:50 CEST 2013 mri_ca_register -invert-and-save transforms/talairach.m3z #-------------------------------------- #@# Remove Neck Thu Aug 8 16:36:11 CEST 2013 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca nu_noneck.mgz #-------------------------------------- #@# SkullLTA Thu Aug 8 16:37:38 CEST 2013 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta #-------------------------------------- #@# SubCort Seg Thu Aug 8 17:17:50 CEST 2013 mri_ca_label -align norm.mgz transforms/talairach.m3z /opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/cc_up.lta sub002 #-------------------------------------- #@# Merge ASeg Thu Aug 8 17:38:36 CEST 2013 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Thu Aug 8 17:38:36 CEST 2013 mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz #-------------------------------------------- #@# Mask BFS Thu Aug 8 17:42:58 CEST 2013 mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz #-------------------------------------------- #@# WM Segmentation Thu Aug 8 17:43:01 CEST 2013 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 Thu Aug 8 17:45:39 CEST 2013 mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz #-------------------------------------------- #@# Tessellate lh Thu Aug 8 17:46:37 CEST 2013 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 Thu Aug 8 17:46:46 CEST 2013 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix #-------------------------------------------- #@# Inflation1 lh Thu Aug 8 17:46:51 CEST 2013 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix #-------------------------------------------- #@# QSphere lh Thu Aug 8 17:47:30 CEST 2013 mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix #-------------------------------------------- #@# Fix Topology lh Thu Aug 8 17:53:01 CEST 2013 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 sub002 lh mris_euler_number ../surf/lh.orig mris_remove_intersection ../surf/lh.orig ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Thu Aug 8 18:08:36 CEST 2013 mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub002 lh #-------------------------------------------- #@# Smooth2 lh Thu Aug 8 18:16:43 CEST 2013 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm #-------------------------------------------- #@# Inflation2 lh Thu Aug 8 18:16:48 CEST 2013 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 Thu Aug 8 18:19:36 CEST 2013 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub002 lh curv sulc #-------------------------------------------- #@# Sphere lh Thu Aug 8 18:19:41 CEST 2013 mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere #-------------------------------------------- #@# Surf Reg lh Thu Aug 8 19:28:39 CEST 2013 mris_register -curv ../surf/lh.sphere /opt/freesurfer/5.3.0/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg #-------------------------------------------- #@# Jacobian white lh Thu Aug 8 20:02:00 CEST 2013 mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Thu Aug 8 20:02:03 CEST 2013 mrisp_paint -a 5 /opt/freesurfer/5.3.0/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv #----------------------------------------- #@# Cortical Parc lh Thu Aug 8 20:02:05 CEST 2013 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub002 lh ../surf/lh.sphere.reg /opt/freesurfer/5.3.0/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot #-------------------------------------------- #@# Make Pial Surf lh Thu Aug 8 20:03:19 CEST 2013 mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub002 lh #-------------------------------------------- #@# Surf Volume lh Thu Aug 8 20:20:22 CEST 2013 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 Thu Aug 8 20:20:22 CEST 2013 pctsurfcon --s sub002 --lh-only #----------------------------------------- #@# Parcellation Stats lh Thu Aug 8 20:20:37 CEST 2013 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 sub002 lh white #----------------------------------------- #@# Cortical Parc 2 lh Thu Aug 8 20:21:03 CEST 2013 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub002 lh ../surf/lh.sphere.reg /opt/freesurfer/5.3.0/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot #----------------------------------------- #@# Parcellation Stats 2 lh Thu Aug 8 20:22:26 CEST 2013 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 sub002 lh white #----------------------------------------- #@# Cortical Parc 3 lh Thu Aug 8 20:22:56 CEST 2013 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub002 lh ../surf/lh.sphere.reg /opt/freesurfer/5.3.0/average/lh.DKTatlas40.gcs ../label/lh.aparc.DKTatlas40.annot #----------------------------------------- #@# Parcellation Stats 3 lh Thu Aug 8 20:24:13 CEST 2013 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 sub002 lh white #-------------------------------------------- #@# Tessellate rh Thu Aug 8 20:24:49 CEST 2013 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 Thu Aug 8 20:24:59 CEST 2013 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix #-------------------------------------------- #@# Inflation1 rh Thu Aug 8 20:25:04 CEST 2013 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix #-------------------------------------------- #@# QSphere rh Thu Aug 8 20:25:50 CEST 2013 mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix #-------------------------------------------- #@# Fix Topology rh Thu Aug 8 20:33:25 CEST 2013 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 sub002 rh mris_euler_number ../surf/rh.orig mris_remove_intersection ../surf/rh.orig ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Thu Aug 8 20:53:51 CEST 2013 mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub002 rh #-------------------------------------------- #@# Smooth2 rh Thu Aug 8 21:02:09 CEST 2013 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm #-------------------------------------------- #@# Inflation2 rh Thu Aug 8 21:02:15 CEST 2013 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 Thu Aug 8 21:05:03 CEST 2013 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub002 rh curv sulc #-------------------------------------------- #@# Sphere rh Thu Aug 8 21:05:09 CEST 2013 mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere #-------------------------------------------- #@# Surf Reg rh Thu Aug 8 22:21:45 CEST 2013 mris_register -curv ../surf/rh.sphere /opt/freesurfer/5.3.0/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg #-------------------------------------------- #@# Jacobian white rh Thu Aug 8 22:58:34 CEST 2013 mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv rh Thu Aug 8 22:58:37 CEST 2013 mrisp_paint -a 5 /opt/freesurfer/5.3.0/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv #----------------------------------------- #@# Cortical Parc rh Thu Aug 8 22:58:41 CEST 2013 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub002 rh ../surf/rh.sphere.reg /opt/freesurfer/5.3.0/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot #-------------------------------------------- #@# Make Pial Surf rh Thu Aug 8 23:00:14 CEST 2013 mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub002 rh #-------------------------------------------- #@# Surf Volume rh Thu Aug 8 23:16:44 CEST 2013 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 Thu Aug 8 23:16:45 CEST 2013 pctsurfcon --s sub002 --rh-only #----------------------------------------- #@# Parcellation Stats rh Thu Aug 8 23:17:00 CEST 2013 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 sub002 rh white #----------------------------------------- #@# Cortical Parc 2 rh Thu Aug 8 23:17:33 CEST 2013 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub002 rh ../surf/rh.sphere.reg /opt/freesurfer/5.3.0/average/rh.destrieux.simple.2009-07-29.gcs ../label/rh.aparc.a2009s.annot #----------------------------------------- #@# Parcellation Stats 2 rh Thu Aug 8 23:18:57 CEST 2013 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 sub002 rh white #----------------------------------------- #@# Cortical Parc 3 rh Thu Aug 8 23:19:22 CEST 2013 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub002 rh ../surf/rh.sphere.reg /opt/freesurfer/5.3.0/average/rh.DKTatlas40.gcs ../label/rh.aparc.DKTatlas40.annot #----------------------------------------- #@# Parcellation Stats 3 rh Thu Aug 8 23:20:34 CEST 2013 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 sub002 rh white #-------------------------------------------- #@# Refine Pial Surfs w/ T2/FLAIR Thu Aug 8 23:21:01 CEST 2013 bbregister --s sub002 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/T2raw.lta --init-fsl --T2 mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/T2.mgz mri_normalize -aseg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/aseg.mgz -sigma 4 -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.white identity.nofile -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.white identity.nofile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/T2.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/T2.mgz cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.woT2.pial mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub002 lh cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.woT2.pial mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub002 rh #-------------------------------------------- #@# Surf Volume lh Fri Aug 9 00:19:15 CEST 2013 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 #-------------------------------------------- #@# Surf Volume rh Fri Aug 9 00:19:17 CEST 2013 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 #-------------------------------------------- #@# Cortical ribbon mask Fri Aug 9 00:19:18 CEST 2013 mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon sub002 #-------------------------------------------- #@# ASeg Stats Fri Aug 9 00:44:43 CEST 2013 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/5.3.0/ASegStatsLUT.txt --subject sub002 #----------------------------------------- #@# AParc-to-ASeg Fri Aug 9 00:47:43 CEST 2013 mri_aparc2aseg --s sub002 --volmask mri_aparc2aseg --s sub002 --volmask --a2009s #----------------------------------------- #@# WMParc Fri Aug 9 00:53:00 CEST 2013 mri_aparc2aseg --s sub002 --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 sub002 --surf-wm-vol --ctab /opt/freesurfer/5.3.0/WMParcStatsLUT.txt --etiv #-------------------------------------------- #@# BA Labels lh Fri Aug 9 01:05:30 CEST 2013 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.label --trgsubject sub002 --trglabel ./lh.BA1.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.label --trgsubject sub002 --trglabel ./lh.BA2.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.label --trgsubject sub002 --trglabel ./lh.BA3a.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.label --trgsubject sub002 --trglabel ./lh.BA3b.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.label --trgsubject sub002 --trglabel ./lh.BA4a.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.label --trgsubject sub002 --trglabel ./lh.BA4p.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.label --trgsubject sub002 --trglabel ./lh.BA6.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.label --trgsubject sub002 --trglabel ./lh.BA44.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.label --trgsubject sub002 --trglabel ./lh.BA45.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.label --trgsubject sub002 --trglabel ./lh.V1.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.label --trgsubject sub002 --trglabel ./lh.V2.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.label --trgsubject sub002 --trglabel ./lh.MT.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.perirhinal.label --trgsubject sub002 --trglabel ./lh.perirhinal.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.thresh.label --trgsubject sub002 --trglabel ./lh.BA1.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.thresh.label --trgsubject sub002 --trglabel ./lh.BA2.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.thresh.label --trgsubject sub002 --trglabel ./lh.BA3a.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.thresh.label --trgsubject sub002 --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.thresh.label --trgsubject sub002 --trglabel ./lh.BA4a.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.thresh.label --trgsubject sub002 --trglabel ./lh.BA4p.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.thresh.label --trgsubject sub002 --trglabel ./lh.BA6.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.thresh.label --trgsubject sub002 --trglabel ./lh.BA44.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.thresh.label --trgsubject sub002 --trglabel ./lh.BA45.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.thresh.label --trgsubject sub002 --trglabel ./lh.V1.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.thresh.label --trgsubject sub002 --trglabel ./lh.V2.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.thresh.label --trgsubject sub002 --trglabel ./lh.MT.thresh.label --hemi lh --regmethod surface mris_label2annot --s sub002 --hemi lh --ctab /opt/freesurfer/5.3.0/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 sub002 --hemi lh --ctab /opt/freesurfer/5.3.0/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 sub002 lh white mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab sub002 lh white #-------------------------------------------- #@# BA Labels rh Fri Aug 9 01:10:42 CEST 2013 mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.label --trgsubject sub002 --trglabel ./rh.BA1.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.label --trgsubject sub002 --trglabel ./rh.BA2.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.label --trgsubject sub002 --trglabel ./rh.BA3a.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.label --trgsubject sub002 --trglabel ./rh.BA3b.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.label --trgsubject sub002 --trglabel ./rh.BA4a.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.label --trgsubject sub002 --trglabel ./rh.BA4p.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.label --trgsubject sub002 --trglabel ./rh.BA6.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.label --trgsubject sub002 --trglabel ./rh.BA44.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.label --trgsubject sub002 --trglabel ./rh.BA45.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.label --trgsubject sub002 --trglabel ./rh.V1.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.label --trgsubject sub002 --trglabel ./rh.V2.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.label --trgsubject sub002 --trglabel ./rh.MT.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.perirhinal.label --trgsubject sub002 --trglabel ./rh.perirhinal.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.thresh.label --trgsubject sub002 --trglabel ./rh.BA1.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.thresh.label --trgsubject sub002 --trglabel ./rh.BA2.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.thresh.label --trgsubject sub002 --trglabel ./rh.BA3a.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.thresh.label --trgsubject sub002 --trglabel ./rh.BA3b.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.thresh.label --trgsubject sub002 --trglabel ./rh.BA4a.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.thresh.label --trgsubject sub002 --trglabel ./rh.BA4p.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.thresh.label --trgsubject sub002 --trglabel ./rh.BA6.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.thresh.label --trgsubject sub002 --trglabel ./rh.BA44.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.thresh.label --trgsubject sub002 --trglabel ./rh.BA45.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.thresh.label --trgsubject sub002 --trglabel ./rh.V1.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.thresh.label --trgsubject sub002 --trglabel ./rh.V2.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.thresh.label --trgsubject sub002 --trglabel ./rh.MT.thresh.label --hemi rh --regmethod surface mris_label2annot --s sub002 --hemi rh --ctab /opt/freesurfer/5.3.0/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 sub002 --hemi rh --ctab /opt/freesurfer/5.3.0/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 sub002 rh white mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab sub002 rh white #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label lh Fri Aug 9 01:15:48 CEST 2013 mris_spherical_average -erode 1 -orig white -t 0.4 -o sub002 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 sub002 lh white #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label rh Fri Aug 9 01:16:04 CEST 2013 mris_spherical_average -erode 1 -orig white -t 0.4 -o sub002 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 sub002 rh white