Diff for "ReconAllDevTable" - Free Surfer Wiki

Differences between revisions 1 and 20 (spanning 19 versions)

FreeSurfer Tutorial: Process Flow

recon-all-dev step	Individual Flag	Input	Command Line	Output
none	none	file.dcm	["mri_convert"] file.dcm orig/001.mgz	orig/001.mgz
["recon-all-dev"] -autorecon1 -subjid subj
	-motioncor	orig/001.mgz	["mri_motion_correct.fsl"] -o rawavg.mgz -wild orig/001.mgz orig/002.mgz	rawavg.mgz
		orig/002.mgz		rawavg.mgz
		rawavg.mgz	["mri_convert"] rawavg.mgz orig.mgz --conform	orig.mgz
	-nuintensitycor	orig.mgz	["mri_nu_correct.mni"] --i orig.mgz --o nu.mgz --n 4	nu.mgz
	-talairach	nu.mgz	["talairach2"] subjid -mgz	transforms/talairach.xfm
	-normalization	nu.mgz	["mri_normalize"] -g 1 nu.mgz T1.mgz	T1.mgz
	-skullstrip	T1.mgz	["mri_watershed"] T1.mgz brainmask.auto.mgz	brainmask.auto.mgz
	-skullstrip	brainmask.auto.mgz	cp brainmask.auto.mgz brainmask.mgz	brainmask.mgz
Check skullstrip (brain.mgz), talairach (transforms/talairach.xfm), and normalization (brain.mgz or T1.mgz - mean wm voxel value = 110)
["recon-all-dev"] -autorecon2 -subjid subj
	-gcareg	brainmask.mgz	["mri_em_register"] -mask brainmask.mgz -p .5 nu.mgz $FREESURFER_HOME/average/RB40_talairach_2005-07-20.gca transforms/talairach.lta	transforms/talairach.lta
	-gcareg	nu.mgz		transforms/talairach.lta
	-canorm	brainmask.mgz	["mri_ca_normalize"] -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB40_talairach_2005-07-20.gca transforms/talairach.lta norm.mgz	norm.mgz
		nu.mgz
		transforms/talairach.lta
	-careg	brainmask.mgz	["mri_ca_register"] -align -mask brainmask.mgz -T transforms/talairach.lta norm.mgz $FREESURFER_HOME/average/RB40_talairach_2005-07-20.gca transforms/talairach.m3z	transforms/talairach.m3z
		transforms/talairach.lta
		norm.mgz
	-rmneck	nu.mgz	["mri_remove_neck"] -radius 25 nu.mgz transforms/talairach.m3z $FREESURFER_HOME/average/RB40_talairach_2005-07-20.gca nu_noneck.mgz	nu_noneck.mgz
	-rmneck	transforms/talairach.m3z		nu_noneck.mgz
	-skull-lta	transforms/talairach.lta	["mri_em_register"] -skull -t transforms/talairach.lta nu_noneck.mgz $FREESURFER_HOME/average/RB40_talairach_with_skull_2005-07-20.gca transforms/talairach_with_skull.lta	transforms/talairach_with_skull.lta
	-skull-lta	nu_noneck.mgz		transforms/talairach_with_skull.lta
	-calabel	norm.mgz	["mri_ca_label"] -align norm.mgz transforms/talairach.m3z $FREESURFER_HOME/average/RB40_talairach_2005-07-20.gca aseg.auto.mgz	aseg.auto.mgz
		transforms/talairach.m3z		aseg.auto.mgz
		aseg.auto.mgz	cp aseg.auto.mgz aseg.mgz	aseg.mgz
	-segstats	aseg.mgz	["mri_segstats"] --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --in mri/orig.mgz --ctab-default --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in-intensity-name orig --in-intensity-units MR --etiv --subject <subjid>	stats/aseg.stats
	-normalization2	brainmask.mgz	["mri_normalize"] -mask brainmask.mgz norm.mgz brain.mgz	brain.mgz
		norm.mgz	["mri_normalize"] -mask brainmask.mgz norm.mgz brain.mgz	brain.mgz
		brain.mgz	["mri_mask"] brain.mgz brainmask.mgz brain.finalsurfs.mgz	brain.finalsurfs.mgz
		brainmask.mgz	["mri_mask"] brain.mgz brainmask.mgz brain.finalsurfs.mgz	brain.finalsurfs.mgz
	-segmentation	brain.mgz	["mri_segment"] brain.mgz wm.mgz	wm.mgz
	-edit_wm_with_aseg	wm.mgz	["mri_edit_wm_with_aseg"] wm.mgz aseg.mgz wm.mgz	wm.mgz
	-edit_wm_with_aseg	aseg.mgz	["mri_edit_wm_with_aseg"] wm.mgz aseg.mgz wm.mgz	wm.mgz
	-fill	wm.mgz	["mri_fill"] -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.mgz wm.mgz filled.mgz	filled.mgz
		aseg.mgz		../scripts/ponscc.cut.log
		transforms/talairach.lta		../scripts/ponscc.cut.log
	-tessellate	filled.mgz	["mri_tessellate"] filled.mgz 255 ../surf/lh.orig.nofix	lh.orig.nofix
	-tessellate	filled.mgz	["mri_tessellate"] filled.mgz 127 ../surf/rh.orig.nofix	rh.orig.nofix
	-smooth1	?h.orig.nofix	["mris_smooth"] -nw ?h.orig.nofix ?h.smoothwm.nofix	?h.smoothwm.nofix
	-inflate1	?h.smoothwm.nofix	["mris_inflate"] -dist 0 -no-save-sulc ?h.smoothwm.nofix ?h.inflated.nofix	?h.inflated.nofix
	-qsphere	?h.inflated.nofix	["mris_sphere"] -w 0 -inflate -in 200 -q -0 ?h.inflated.nofix ?h.inflated.nofix ?h.qsphere.nofix	?h.qsphere.nofix
	-fix	?h.orig.nofix	cp ?h.orig.nofix ?h.orig	?h.orig
		?h.inflated.nofix	cp ?h.inflated.nofix ?h.inflated	?h.inflated
		?h.qsphere.nofix	["mris_fix_topology"] -errors -mgz -sphere qsphere.nofix -ga <subjid> ?h	?h.orig
	-euler	?h.orig	["mris_euler_number"] ?h.orig	?h.orig.euler
	-smooth2	?h.orig	["mris_smooth"] ?h.orig ?h.smoothwm	?h.smoothwm
	-inflate2	?h.smoothwm	["mris_inflate"] -dist 0 ?h.smoothwm ?h.inflated	?h.inflated
	-inflate2	?h.smoothwm	["mris_inflate"] -dist 0 ?h.smoothwm ?h.inflated	?h.sulc
	-finalsurfs	brain.finalsurfs.mgz	["mris_make_surfaces"] -mgz -w 0 -T1 brain.finalsurfs.mgz subj ?h	?h.white
		brain.finalsurfs.mgz		?h.pial
		?h.orig
		?h.orig		?h.thickness
	?h.sulc
	-cortribbon	orig.mgz	["mri_surf2vol"] --mkmask --hemi ?h --fillribbon --template orig.mgz --volregidentity subj --outvol ?h.ribbon.mgz	?h.ribbon.mgz
		?h.white
?h.pial
Check final surfaces tkmedit subj wm.mgz ?h.white brain.mgz
["recon-all"] -autorecon3 -subjid subj
	-sphere	?h.inflated	["mris_sphere"] -w 0 ?h.inflated ?h.sphere	?h.sphere
	-surfreg	?h.sphere	["mris_register"] -w 0 -curv ?h.sphere $AvgTif ?h.sphere.reg	?h.sphere.reg
	-contrasurfreg	rh.sphere	["mris_register"] -w 0 -curv -reverse rh.sphere $AvgTif rh.lh.sphere.reg	rh.lh.sphere.reg
	-contrasurfreg	lh.sphere	["mris_register"] -w 0 -curv -reverse lh.sphere $AvgTif lh.rh.sphere.reg	lh.rh.sphere.reg
	-avgcurv	?h.sphere.reg	["mrisp_paint"] -a 5 $AvgTif#6 ?h.sphere.reg ?h.avg_curv	?h.avg_curv
	-cortparc	?h.sphere.reg	["mris_ca_label"] -t $CPAnnotTable subj ?h sphere.reg $CPAtlas ?h.aparc.annot	label/?h.aparc.annot
	-parcstats	label/?h.aparc.annot	["mris_anatomical_stats"] -f scripts/?h.aparc.stats -b -a label/?h.aparc.annot subj ?h	stats/?h.aparc.stats

Click here to see a table of OtherUsefulFlags

-  ⇤ ← Revision 1 as of 2006-01-09 17:58:32 → 
  Size: 7565
  Editor: JenniPacheco
  Comment:
+   ← Revision 20 as of 2006-01-10 16:54:22 → ⇥
  Size: 9422
  Editor: JenniPacheco
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
+#acl AdminGroup:read,write,delete,revert All:read
-Line 3:
+Line 5:
-||<rowbgcolor='#80FF80'>'''recon-all step'''||'''Individual Flag'''||'''Input'''||'''Command Line'''||'''Output'''||
+||<rowbgcolor='#80FF80'>'''recon-all-dev step'''||'''Individual Flag'''||'''Input'''||'''Command Line'''||'''Output'''||
-Line 6:
+Line 7:
-||<|10(bgcolor='#FFFFE0'>["recon-all"] -autorecon1 -subjid subj||
||<|3(bgcolor='#FFFFE0'>-motioncor||<bgcolor='#E0E0FF'>orig/001.mgz||<|2(bgcolor='#E0E0FF'>["mri_motion_correct2"] -i orig/001.mgz -i orig/002.mgz -o rawavg.mgz||<|2(bgcolor='#E0E0FF'>rawavg.mgz||
+||<|9(bgcolor='#FFFFE0'>["recon-all-dev"] -autorecon1 -subjid subj||
||<|3(bgcolor='#FFFFE0'>-motioncor||<bgcolor='#E0E0FF'>orig/001.mgz||<|2(bgcolor='#E0E0FF'>["mri_motion_correct.fsl"] -o rawavg.mgz -wild orig/001.mgz orig/002.mgz ||<|2(bgcolor='#E0E0FF'>rawavg.mgz||
-Line 10:
+Line 11:
-||<|3(bgcolor='#FFFFE0'>-nuintensitycor||<bgcolor='#E0E0FF'>orig.mgz||<bgcolor='#E0E0FF'>["mri_convert"] orig.mgz nu0.mnc||<bgcolor='#E0E0FF'>nu0.mnc||
||<rowbgcolor='#E0E0FF'>nu0.mnc||(4 iterations of) ["nu_correct"] -clobber nu0.mnc nu1.mnc||nu4.mnc||
||<rowbgcolor='#E0E0FF'>nu4.mnc||["mri_convert"] nu4.mnc nu.mgz||nu.mgz||
+||<bgcolor='#FFFFE0'>-nuintensitycor||<bgcolor='#E0E0FF'>orig.mgz||<bgcolor='#E0E0FF'>["mri_nu_correct.mni"] --i orig.mgz --o nu.mgz --n 4||<bgcolor='#E0E0FF'>nu.mgz||
-Line 14:
+Line 13:
-||<bgcolor='#FFFFE0'>-normalization||<bgcolor='#E0E0FF'>nu.mgz||<bgcolor='#E0E0FF'>["mri_normalize"] nu.mgz T1.mgz||<bgcolor='#E0E0FF'>T1.mgz||
||<bgcolor='#FFFFE0'>-skullstrip||<bgcolor='#E0E0FF'>T1.mgz||<bgcolor='#E0E0FF'>["mri_watershed"] T1.mgz brain.mgz||<bgcolor='#E0E0FF'>brain.mgz||
+||<bgcolor='#FFFFE0'>-normalization||<bgcolor='#E0E0FF'>nu.mgz||<bgcolor='#E0E0FF'>["mri_normalize"] -g 1 nu.mgz T1.mgz||<bgcolor='#E0E0FF'>T1.mgz||
||<|2(bgcolor='#FFFFE0'>-skullstrip||<bgcolor='#E0E0FF'>T1.mgz||<bgcolor='#E0E0FF'>["mri_watershed"] T1.mgz brainmask.auto.mgz||<bgcolor='#E0E0FF'>brainmask.auto.mgz||
||<rowbgcolor='#E0E0FF'>brainmask.auto.mgz||<bgcolor='#E0E0FF'>cp brainmask.auto.mgz brainmask.mgz||<bgcolor='#E0E0FF'>brainmask.mgz||
 Line 17:
-||<|36(bgcolor='#FFFFE0'>["recon-all"] -autorecon2 -subjid subj||
||<|2(bgcolor='#FFFFE0'>-gcareg||<bgcolor='#E0E0FF'>brain.mgz||<|2(bgcolor='#E0E0FF'>["mri_em_register"] -mask brain.mgz -p .5 -fsamples fsamples.mgz nu.mgz $GCA transforms/talairach.lta||<|2(bgcolor='#E0E0FF'>transforms/talairach.lta||
+||<|46(bgcolor='#FFFFE0'>["recon-all-dev"] -autorecon2 -subjid subj||
||<|2(bgcolor='#FFFFE0'>-gcareg||<bgcolor='#E0E0FF'>brainmask.mgz||<|2(bgcolor='#E0E0FF'>["mri_em_register"] -mask brainmask.mgz -p .5 nu.mgz $FREESURFER_HOME/average/RB40_talairach_2005-07-20.gca transforms/talairach.lta||<|2(bgcolor='#E0E0FF'>transforms/talairach.lta||
 Line 20:
-||<|3(bgcolor='#FFFFE0'>-canorm||<bgcolor='#E0E0FF'>brain.mgz||<|3(bgcolor='#E0E0FF'>["mri_ca_normalize"] -mask brain.mgz nu.mgz $GCA transforms/talairach.lta norm.mgz||<|3(bgcolor='#E0E0FF'>norm.mgz||
+||<|3(bgcolor='#FFFFE0'>-canorm||<bgcolor='#E0E0FF'>brainmask.mgz||<|3(bgcolor='#E0E0FF'>["mri_ca_normalize"] -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB40_talairach_2005-07-20.gca transforms/talairach.lta norm.mgz||<|3(bgcolor='#E0E0FF'>norm.mgz||
 Line 23:
-||<|3(bgcolor='#FFFFE0'>-careg||<bgcolor='#E0E0FF'>brain.mgz||<|3(bgcolor='#E0E0FF'>["mri_ca_register"] -cross-sequence -mask brain.mgz -T transforms/talairach.lta norm.mgz $GCA transforms/talairach.m3z||<|3(bgcolor='#E0E0FF'>transforms/talairach.m3z||
+||<|3(bgcolor='#FFFFE0'>-careg||<bgcolor='#E0E0FF'>brainmask.mgz||<|3(bgcolor='#E0E0FF'>["mri_ca_register"] -align -mask brainmask.mgz -T transforms/talairach.lta norm.mgz $FREESURFER_HOME/average/RB40_talairach_2005-07-20.gca transforms/talairach.m3z||<|3(bgcolor='#E0E0FF'>transforms/talairach.m3z||
 Line 26:
-||<|2(bgcolor='#FFFFE0'>-calabel||<bgcolor='#E0E0FF'>norm.mgz||<|2(bgcolor='#E0E0FF'>["mri_ca_label"] -cross-sequence norm.mgz transforms/talairach.m3z $GCA aseg.mgz||<|2(bgcolor='#E0E0FF'>aseg.mgz||
+||<|2(bgcolor='#FFFFE0'>-rmneck||<bgcolor='#E0E0FF'>nu.mgz||<|2(bgcolor='#E0E0FF'>["mri_remove_neck"] -radius 25 nu.mgz transforms/talairach.m3z $FREESURFER_HOME/average/RB40_talairach_2005-07-20.gca nu_noneck.mgz||<|2(bgcolor='#E0E0FF'>nu_noneck.mgz||
 Line 28:
-||<bgcolor='#FFFFE0'>-segstats||<bgcolor='#E0E0FF'>aseg.mgz||<bgcolor='#E0E0FF'>["mri_segstats"] --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --in mri/orig.mgz --ctab-default --excludeid 0 --brain-vol-from-seg --brainmask mri/brain.mgz||<bgcolor='#E0E0FF'>stats/aseg.stats||
||<|4(bgcolor='#FFFFE0'>-normalization2||<bgcolor='#E0E0FF'>brain.mgz||<|2(bgcolor='#E0E0FF'>["mri_normalize"] -mask brain.mgz nu.mgz T1.mgz||<|2(bgcolor='#E0E0FF'>T1.mgz||
||<rowbgcolor='#E0E0FF'>nu.mgz||
||<rowbgcolor='#E0E0FF'>T1.mgz||<|2(>["mri_mask"] T1.mgz brain.mgz brain.mgz||<|2(>brain.mgz||
||<rowbgcolor='#E0E0FF'>brain.mgz||
+||<|2(bgcolor='#FFFFE0'>-skull-lta||<bgcolor='#E0E0FF'>transforms/talairach.lta||<|2(bgcolor='#E0E0FF'>["mri_em_register"] -skull -t transforms/talairach.lta nu_noneck.mgz $FREESURFER_HOME/average/RB40_talairach_with_skull_2005-07-20.gca transforms/talairach_with_skull.lta||<|2(bgcolor='#E0E0FF'>transforms/talairach_with_skull.lta||
||<rowbgcolor='#E0E0FF'>nu_noneck.mgz||
||<|3(bgcolor='#FFFFE0'>-calabel||<bgcolor='#E0E0FF'>norm.mgz||<|2(bgcolor='#E0E0FF'>["mri_ca_label"] -align norm.mgz transforms/talairach.m3z $FREESURFER_HOME/average/RB40_talairach_2005-07-20.gca aseg.auto.mgz||<|2(bgcolor='#E0E0FF'>aseg.auto.mgz||
||<rowbgcolor='#E0E0FF'>transforms/talairach.m3z||
||<rowbgcolor='#E0E0FF'>aseg.auto.mgz||<bgcolor='#E0E0FF'>cp aseg.auto.mgz aseg.mgz||<bgcolor='#E0E0FF'>aseg.mgz||
||<bgcolor='#FFFFE0'>-segstats||<bgcolor='#E0E0FF'>aseg.mgz||<bgcolor='#E0E0FF'>["mri_segstats"] --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --in mri/orig.mgz --ctab-default --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in-intensity-name orig --in-intensity-units MR --etiv --subject <subjid>||<bgcolor='#E0E0FF'>stats/aseg.stats||
||<|4(bgcolor='#FFFFE0'>-normalization2||<bgcolor='#E0E0FF'>brainmask.mgz||<|2(bgcolor='#E0E0FF'>["mri_normalize"] -mask brainmask.mgz norm.mgz brain.mgz||<|2(bgcolor='#E0E0FF'>brain.mgz||
||<rowbgcolor='#E0E0FF'>norm.mgz||
||<rowbgcolor='#E0E0FF'>brain.mgz||<|2(>["mri_mask"] brain.mgz brainmask.mgz brain.finalsurfs.mgz||<|2(>brain.finalsurfs.mgz||
||<rowbgcolor='#E0E0FF'>brainmask.mgz||
-Line 36:
+Line 41:
-||<|2(bgcolor='#FFFFE0'>-fill||<bgcolor='#E0E0FF'>wm.mgz||<|2(bgcolor='#E0E0FF'>["mri_fill"] -a ../scripts/ponscc.cut.log -xform transforms/talairach.xfm -segmentation aseg.mgz wm.mgz filled.mgz||<bgcolor='#E0E0FF'>filled.mgz||
||<rowbgcolor='#E0E0FF'>aseg.mgz||../scripts/ponscc.cut.log||
||<|2((bgcolor='#FFFFE0'>-tessellate||<|2(bgcolor='#E0E0FF'>filled.mgz||<bgcolor='#E0E0FF'>["mri_tessellate"] filled.mgz 255 ../surf/lh.orig||<bgcolor='#E0E0FF'>lh.orig||
||<rowbgcolor='#E0E0FF'>["mri_tessellate"] filled.mgz 127 ../surf/rh.orig||rh.orig||
||<bgcolor='#FFFFE0'>-smooth1||<bgcolor='#E0E0FF'>?h.orig||<bgcolor='#E0E0FF'>["mris_smooth"] ?h.orig ?h.smoothwm||<bgcolor='#E0E0FF'>?h.smoothwm||
||<bgcolor='#FFFFE0'>-inflate1||<bgcolor='#E0E0FF'>?h.smoothwm||<bgcolor='#E0E0FF'>["mris_inflate"] ?h.smoothwm ?h.inflated||<bgcolor='#E0E0FF'>?h.inflated||
||<bgcolor='#FFFFE0'>-qsphere||<bgcolor='#E0E0FF'>?h.inflated||<bgcolor='#E0E0FF'>["mris_sphere"] -w 0 -inflate -in 200 -q ?h.inflated ?h.qsphere||<bgcolor='#E0E0FF'>?h.qsphere||
||<bgcolor='#FFFFE0'>-fix||<bgcolor='#E0E0FF'>?h.qsphere||<bgcolor='#E0E0FF'>["mris_fix_topology"] subj ?h||<bgcolor='#E0E0FF'>?h.orig||
+||<|3(bgcolor='#FFFFE0'>-fill||<bgcolor='#E0E0FF'>wm.mgz||<|3(bgcolor='#E0E0FF'>["mri_fill"] -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.mgz wm.mgz filled.mgz||<bgcolor='#E0E0FF'>filled.mgz||
||<rowbgcolor='#E0E0FF'>aseg.mgz||<|2(bgcolor='#E0E0FF'>../scripts/ponscc.cut.log||
||<rowbgcolor='#E0E0FF'>transforms/talairach.lta||
||<|2((bgcolor='#FFFFE0'>-tessellate||<|2(bgcolor='#E0E0FF'>filled.mgz||<bgcolor='#E0E0FF'>["mri_tessellate"] filled.mgz 255 ../surf/lh.orig.nofix||<bgcolor='#E0E0FF'>lh.orig.nofix||
||<rowbgcolor='#E0E0FF'>["mri_tessellate"] filled.mgz 127 ../surf/rh.orig.nofix||rh.orig.nofix||
||<bgcolor='#FFFFE0'>-smooth1||<bgcolor='#E0E0FF'>?h.orig.nofix||<bgcolor='#E0E0FF'>["mris_smooth"] -nw ?h.orig.nofix ?h.smoothwm.nofix||<bgcolor='#E0E0FF'>?h.smoothwm.nofix||
||<bgcolor='#FFFFE0'>-inflate1||<bgcolor='#E0E0FF'>?h.smoothwm.nofix||<bgcolor='#E0E0FF'>["mris_inflate"] -dist 0 -no-save-sulc ?h.smoothwm.nofix ?h.inflated.nofix||<bgcolor='#E0E0FF'>?h.inflated.nofix||
||<bgcolor='#FFFFE0'>-qsphere||<bgcolor='#E0E0FF'>?h.inflated.nofix||<bgcolor='#E0E0FF'>["mris_sphere"] -w 0 -inflate -in 200 -q -0 ?h.inflated.nofix ?h.inflated.nofix ?h.qsphere.nofix||<bgcolor='#E0E0FF'>?h.qsphere.nofix||
||<|3(bgcolor='#FFFFE0'>-fix||<bgcolor='#E0E0FF'>?h.orig.nofix||<bgcolor='#E0E0FF'>cp ?h.orig.nofix ?h.orig||<bgcolor='#E0E0FF'>?h.orig||
||<bgcolor='#E0E0FF'>?h.inflated.nofix||<bgcolor='#E0E0FF'>cp ?h.inflated.nofix ?h.inflated||<bgcolor='#E0E0FF'>?h.inflated||
||<bgcolor='#E0E0FF'>?h.qsphere.nofix||<bgcolor='#E0E0FF'>["mris_fix_topology"] -errors -mgz -sphere qsphere.nofix -ga <subjid> ?h||<bgcolor='#E0E0FF'>?h.orig||
-Line 46:
+Line 54:
-||<bgcolor='#FFFFE0'>-inflate2||<bgcolor='#E0E0FF'>?h.smoothwm||<bgcolor='#E0E0FF'>["mris_inflate"] ?h.smoothwm ?h.inflated||<bgcolor='#E0E0FF'>?h.inflated||
||<|3(bgcolor='#FFFFE0'>-finalsurfs||<bgcolor='#E0E0FF'>brain.mgz||<|3(bgcolor='#E0E0FF'>["mris_make_surfaces"] -w 0 subj ?h||<bgcolor='#E0E0FF'>?h.white||
||<|2(rowbgcolor='#E0E0FF'>?h.orig||?h.pial||
+||<|2(bgcolor='#FFFFE0'>-inflate2||<|2(bgcolor='#E0E0FF'>?h.smoothwm||<|2(bgcolor='#E0E0FF'>["mris_inflate"] -dist 0 ?h.smoothwm ?h.inflated||<bgcolor='#E0E0FF'>?h.inflated||
||<(rowbgcolor='#E0E0FF'>?h.sulc||
||<|4(bgcolor='#FFFFE0'>-finalsurfs||<|2(bgcolor='#E0E0FF'>brain.finalsurfs.mgz||<|4(bgcolor='#E0E0FF'>["mris_make_surfaces"] -mgz -w 0 -T1 brain.finalsurfs.mgz subj ?h||<bgcolor='#E0E0FF'>?h.white||
||<rowbgcolor='#E0E0FF'>?h.pial||
||<|2(rowbgcolor='#E0E0FF'>?h.orig||
-Line 50:
+Line 60:
+||<rowbgcolor='#E0E0FF'>?h.sulc||