Diff for "ReconAllDevTable" - Free Surfer Wiki

Differences between revisions 143 and 159 (spanning 16 versions)

FreeSurfer Tutorial: Process Flow

This table shows the recon-all steps for the current dev version of FreeSurfer. See ReconAllTableStableV5.0 to see a process flow for the latest stable version of FreeSurfer.

Click here to see this information presented in a block diagram format and here for a process v. files table.

See also the OtherUsefulFlags for other recon-all options.

recon-all step	Individual Flag	Input	Command Line	Output
recon-all -autorecon1 -subjid <subjid>
	-i <invol1> -i <invol2>	invol1.dcm	mri_convert invol1.dcm orig/001.mgz	orig/001.mgz
	-i <invol1> -i <invol2>	invol2.dcm	mri_convert invol2.dcm orig/002.mgz	orig/002.mgz
	-motioncor	orig/001.mgz	mri_robust_template --mov 001.mgz 002.mgz --average 1 --template rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --subsample 200	rawavg.mgz
		orig/002.mgz		rawavg.mgz
		rawavg.mgz	mri_convert rawavg.mgz orig.mgz --conform	orig.mgz
		orig.mgz	mri_add_xform_to_header -c transforms/talairach.xfm orig.mgz orig.mgz	orig.mgz
	-nuintensitycor	orig.mgz	mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2	nu.mgz
	-talairach	nu.mgz	talairach_avi --i nu.mgz --xfm transforms/talairach.auto.xfm	transforms/talairach.auto.xfm
		transforms/talairach.auto.xfm	cp transforms/talairach.auto.xfm transforms/talairach.xfm	transforms/talairach.xfm
		transforms/talairach.xfm	talairach_afd -T 0.005 -xfm transforms/talairach.xfm	transforms/talairach.xfm
			awk -f $FREESURFER_HOME/bin/extract_talairach_avi_QA.awk transforms/talairach_avi.log	transforms/talairach_avi.log
	-normalization	nu.mgz	mri_normalize -g 1 nu.mgz T1.mgz	T1.mgz
	-skullstrip	nu.mgz	mri_em_register -skull nu.mgz $FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta	transforms/talairach_with_skull.lta
		T1.mgz	mri_watershed -T1 -brain_atlas $FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz	brainmask.auto.mgz
		T1.mgz	mri_gcut -110 -mult brainmask.auto.mgz T1.mgz brainmask.auto.mgz	brainmask.auto.mgz
		brainmask.auto.mgz		brainmask.auto.mgz
		brainmask.auto.mgz	cp brainmask.auto.mgz brainmask.mgz	brainmask.mgz

recon-all -autorecon2 -subjid <subjid>
	-gcareg	brainmask.mgz	mri_em_register -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB_all_2008-03-26.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/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz	norm.mgz
		nu.mgz
		transforms/talairach.lta
	-careg	brainmask.mgz	mri_ca_register -align-after -nobigventricles -mask brainmask.mgz -T transforms/talairach.lta norm.mgz $FREESURFER_HOME/average/RB_all_2008-03-26.gca transforms/talairach.m3z	transforms/talairach.m3z
		transforms/talairach.lta
		norm.mgz
	-careginv	transforms/talairach.m3z	mri_ca_register -invert-and-save transforms/talairach.m3z	transforms/talairach.m3z.inv.x.mgz
				transforms/talairach.m3z.inv.y.mgz
				transforms/talairach.m3z.inv.z.mgz
	-rmneck	nu.mgz	mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2008-03-26.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/RB_all_withskull_2008-03-26.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 -nobigventricles norm.mgz transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz	aseg.auto_noCCseg.mgz
		transforms/talairach.m3z		aseg.auto_noCCseg.mgz
		aseg.auto_noCCseg.mgz	mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz <subjid>	aseg.auto.mgz
		aseg.auto.mgz	cp aseg.auto.mgz aseg.mgz	aseg.mgz
	-normalization2	brainmask.mgz	mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz	brain.mgz
		norm.mgz
		aseg.mgz
	-maskbfs	brain.mgz	mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz	brain.finalsurfs.mgz
	-maskbfs	brainmask.mgz	mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz	brain.finalsurfs.mgz
	-segmentation	brain.mgz	mri_segment brain.mgz wm.seg.mgz	wm.seg.mgz
		wm.seg.mgz	mri_edit_wm_with_aseg wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz	wm.asegedit.mgz
		aseg.mgz
		brain.mgz
		wm.asegedit.mgz	mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz	wm.mgz
		norm.mgz	mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz	wm.mgz
	-fill	wm.mgz	mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz	filled.mgz
		aseg.auto_noCCseg.mgz		../scripts/ponscc.cut.log
		transforms/talairach.lta		../scripts/ponscc.cut.log
	-tessellate	filled.mgz	mri_pretess filled.mgz 255 norm.mgz filled-pretess255.mgz	filled-pretess255.mgz
		norm.mgz	mri_pretess filled.mgz 255 norm.mgz filled-pretess255.mgz	filled-pretess255.mgz
		filled-pretess255.mgz	mri_tessellate filled-pretess255.mgz 255 lh.orig.nofix	lh.orig.nofix
		filled.mgz	mri_pretess filled.mgz 127 norm.mgz filled-pretess127.mgz	filled-pretess127.mgz
		norm.mgz	mri_pretess filled.mgz 127 norm.mgz filled-pretess127.mgz	filled-pretess127.mgz
		filled-pretess127.mgz	mri_tessellate filled-pretess127.mgz 127 rh.orig.nofix	rh.orig.nofix
		?h.orig.nofix	mris_extract_main_component ?h.orig.nofix ?h.orig.nofix	?h.orig.nofix
			rm -f filled-pretess255.mgz filled-pretess127.mgz
	-smooth1	?h.orig.nofix	mris_smooth -nw ?h.orig.nofix ?h.smoothwm.nofix	?h.smoothwm.nofix
	-inflate1	?h.smoothwm.nofix	mris_inflate -no-save-sulc ?h.smoothwm.nofix ?h.inflated.nofix	?h.inflated.nofix
	-qsphere	?h.inflated.nofix	mris_sphere -q ?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 -mgz -sphere qsphere.nofix -ga <subjid> ?h	?h.orig
		?h.orig	mris_euler_number ?h.orig	?h.orig
		?h.orig	mris_remove_intersection ?h.orig ?h.orig	?h.orig
			rm ?h.inflated
	-white	aseg.mgz, brain.finalsurfs.mgz, wm.mgz, filled.mgz	mris_make_surfaces -whiteonly -noaparc -mgz -T1 brain.finalsurfs <subjid> ?h	?h.white
		?h.orig
				?h.curv
				?h.area
				?h.cortex.label
	-surfvolume	?h.area	mris_calc -o ?h.area.mid ?h.area add ?h.area.pial	?h.area.mid
		?h.area.pial	mris_calc -o ?h.area.mid ?h.area add ?h.area.pial	?h.area.mid
		?h.area.mid	mris_calc -o ?h.area.mid ?h.area.mid div 2	?h.area.mid
		?h.area.mid	mris_calc -o ?h.volume ?h.area.mid mul ?h.thickness	?h.volume
		?h.thickness	mris_calc -o ?h.volume ?h.area.mid mul ?h.thickness	?h.volume
	-smooth2	?h.white	mris_smooth -n 3 -nw ?h.white ?h.smoothwm	?h.smoothwm
	-inflate2	?h.smoothwm	mris_inflate ?h.smoothwm ?h.inflated	?h.inflated
		?h.smoothwm	mris_inflate ?h.smoothwm ?h.inflated	?h.sulc
?h.inflated		mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ?h.inflated	?h.inflated.H
?h.inflated			?h.inflated.K

recon-all -autorecon3 -subjid <subjid>
	-sphere	?h.inflated,?h.smoothwm	mris_sphere ?h.inflated ?h.sphere	?h.sphere
	-surfreg	?h.sphere	mris_register -curv ?h.sphere $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif ?h.sphere.reg	?h.sphere.reg
	-jacobian_white	?h.white	mris_jacobian ?h.white ?h.sphere.reg ?h.jacobian_white	?h.jacobian_white
	-jacobian_white	?h.sphere.reg	mris_jacobian ?h.white ?h.sphere.reg ?h.jacobian_white	?h.jacobian_white
	-avgcurv	?h.sphere.reg	mrisp_paint -a 5 $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif#6 ?h.sphere.reg ?h.avg_curv	?h.avg_curv
	-cortparc	aseg.mgz	mris_ca_label -aseg mri/aseg.mgz <subjid> ?h ?h.sphere.reg $FREESURFER_HOME/average/?h.curvature.buckner40.filled.desikan_killiany.2007-06-20gcs ?h.aparc.annot	label/?h.aparc.annot
	-cortparc	?h.sphere.reg		label/?h.aparc.annot
	-parcstats	label/?h.aparc.annot	mris_anatomical_stats -mgz -f stats/?h.aparc.stats -b -a label/?h.aparc.annot -c label/aparc.annot.ctab <subjid> ?h	stats/?h.aparc.stats label/aparc.annot.ctab
	-cortparc2	aseg.mgz	mris_ca_label -aseg aseg.mgz <subjid> ?h ?h.sphere.reg $FREESURFER_HOME/average/?h.destrieux.simple.2009-07-29.gcs label/?h.aparc.a2009s.annot	label/?h.aparc.a2009s.annot
	-cortparc2	?h.sphere.reg		label/?h.aparc.a2009s.annot
	-parcstats2	label/?h.aparc.a2009s.annot	mris_anatomical_stats -mgz -f stats/?h.aparc.a2009s.stats -b -a label/?h.aparc.a2009s.annot -c label/aparc.annot.a2009s.ctab <subjid> ?h	stats/?h.aparc.a2009s.stats stats/aparc.annot.a2009s.ctab
	-cortribbon	aseg.mgz	mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance <subjid>	?h.ribbon.mgz
		?h.white
		?h.pial
	-segstats	aseg.mgz	mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --totalgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --ctab $FREESURFER_HOME/ASegStatsLUT.txt --subject <subjid>	stats/aseg.stats
	-aparc2aseg	aseg.mgz	mri_aparc2aseg --s <subjid> --ribbon	aparc+aseg.mgz
		?h.ribbon.mgz
		label/?h.aparc.annot
		aseg.mgz	mri_aparc2aseg --s <subjid> --ribbon --a2009s	aparc.a2009s+aseg.mgz
		?h.ribbon.mgz
		label/?h.aparc.a2009s.annot
	-wmparc	aparc+aseg.mgz	mri_aparc2aseg --s <subjid> --labelwm --hypo-as-wm --rip-unknown --ribbon --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz	wmparc.mgz
	-wmparc	wmparc.mgz	mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject <subjid> --surf-wm-vol --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt	stats/wmparc.stats
	-balabels	?h.sphere.reg	mri_label2label --srcsubject fsaverage --srclabel fsaverage/label/?h.BA.label --trgsubject <subjid> --trglabel ?h.BA.label --hemi ?h --regmethod surface	label/?h.BA*.label
	-label-exvivo-ec	?h.sphere.reg	mris_spherical_average -erode 1 -orig white -t 0.4 -o <subjid> label ?h.entorhinal ?h sphere.reg ?h.EC_average ?h.entorhinal_exvivo.label	label/?h.entorhinal_exvivo.label

-  ⇤ ← Revision 143 as of 2009-10-05 19:39:12 → 
  Size: 16193
  Editor: NickSchmansky
  Comment: moved mri_segstats from autorecon2 to autorecon3
+   ← Revision 159 as of 2010-11-03 12:10:36 → ⇥
  Size: 13805
  Editor: NickSchmansky
  Comment: changed -finalsurfs stage to -white (pial and thickness now created in -pial stage)
-Deletions are marked like this.
+Additions are marked like this.
 Line 2:
-Line 4:
+Line 3:
-This table shows the recon-all steps for the current '''dev''' version of FreeSurfer. See ReconAllStableTablev4 to see a process flow for the latest '''stable''' version of FreeSurfer.
+This table shows the recon-all steps for the current '''dev''' version of FreeSurfer. See ReconAllTableStableV5.0 to see a process flow for the latest '''stable''' version of FreeSurfer.
-Line 9:
+Line 8:
-||<rowbgcolor='#80FF80'>'''recon-all step'''||'''Individual Flag'''||'''Input'''||'''Command Line'''||'''Output'''||
||<|16(bgcolor='#FFFFE0'>'''[[recon-all]] -autorecon1 -subjid <subjid>'''||
||<|2(bgcolor='#FFFFE0'>-i <invol1> -i <invol2>||<bgcolor='#E0E0FF'>invol1.dcm||<bgcolor='#E0E0FF'>[[mri_convert]] invol1.dcm orig/001.mgz||<bgcolor='#E0E0FF'>orig/001.mgz||
||<bgcolor='#E0E0FF'>invol2.dcm||<bgcolor='#E0E0FF'>[[mri_convert]] invol2.dcm orig/002.mgz||<bgcolor='#E0E0FF'>orig/002.mgz||
||<|4(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||
||<rowbgcolor='#E0E0FF'>orig/002.mgz||
||<rowbgcolor='#E0E0FF'>rawavg.mgz||[[mri_convert]] rawavg.mgz orig.mgz --conform||orig.mgz||
||<rowbgcolor='#E0E0FF'>orig.mgz||[[mri_add_xform_to_header]] -c transforms/talairach.xfm orig.mgz orig.mgz||orig.mgz||
||<bgcolor='#FFFFE0'>-[[nuintensitycor]]||<bgcolor='#E0E0FF'>orig.mgz||<bgcolor='#E0E0FF'>[[mri_nu_correct.mni]] --i orig.mgz --o nu.mgz --n 2||<bgcolor='#E0E0FF'>nu.mgz||
||<|4(bgcolor='#FFFFE0'>-[[talairach]]||<bgcolor='#E0E0FF'>nu.mgz||<bgcolor='#E0E0FF'>[[talairach_avi]] --i nu.mgz --xfm transforms/talairach.auto.xfm||<bgcolor='#E0E0FF'>transforms/talairach.auto.xfm||
||<rowbgcolor='#E0E0FF'>transforms/talairach.auto.xfm||cp transforms/talairach.auto.xfm transforms/talairach.xfm||<bgcolor='#E0E0FF'>transforms/talairach.xfm||
||<rowbgcolor='#E0E0FF'>transforms/talairach.xfm||<bgcolor='#E0E0FF'>[[talairach_afd]] -T 0.005 -xfm transforms/talairach.xfm||<bgcolor='#E0E0FF'>transforms/talairach.xfm||
||<rowbgcolor='#E0E0FF'>||awk -f $FREESURFER_HOME/bin/extract_talairach_avi_QA.awk transforms/talairach_avi.log||<bgcolor='#E0E0FF'>transforms/talairach_avi.log||
||<bgcolor='#FFFFE0'>-[[normalization]]||<bgcolor='#E0E0FF'>nu.mgz||<bgcolor='#E0E0FF'>[[mri_normalize]] -g 1 nu.mgz T1.mgz||<bgcolor='#E0E0FF'>T1.mgz||
||<|3(bgcolor='#FFFFE0'>-[[skullstrip]]||<bgcolor='#E0E0FF'>nu.mgz||<bgcolor='#E0E0FF'>[[mri_em_register]] -skull nu.mgz $FREESURFER_HOME/average/RB_all_withskull_2007-08-08.gca transforms/talairach_with_skull.lta||<bgcolor='#E0E0FF'>transforms/talairach_with_skull.lta||
||<bgcolor='#E0E0FF'>T1.mgz||<bgcolor='#E0E0FF'>[[mri_watershed]] -T1 -brain_atlas $FREESURFER_HOME/average/RB_all_withskull_2007-08-08.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz||<bgcolor='#E0E0FF'>brainmask.auto.mgz||
||<rowbgcolor='#E0E0FF'>brainmask.auto.mgz||cp brainmask.auto.mgz brainmask.mgz||<bgcolor='#E0E0FF'>brainmask.mgz||
||<rowbgcolor='#E0E0FF'>||<bgcolor='#E0E0FF'>||<bgcolor='#E0E0FF'>||<bgcolor='#E0E0FF'>||<bgcolor='#E0E0FF'>||
||<|68(bgcolor='#FFFFE0'>'''[[recon-all]] -autorecon2 -subjid <subjid>'''||
||<|2(bgcolor='#FFFFE0'>-[[gcareg]]||<bgcolor='#E0E0FF'>brainmask.mgz||<|2(bgcolor='#E0E0FF'>[[mri_em_register]] -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB_all_2007-08-08.gca transforms/talairach.lta||<|2(bgcolor='#E0E0FF'>transforms/talairach.lta||
||<rowbgcolor='#E0E0FF'>nu.mgz||
||<|3(bgcolor='#FFFFE0'>-[[canorm]]||<bgcolor='#E0E0FF'>brainmask.mgz||<|3(bgcolor='#E0E0FF'>[[mri_ca_normalize]] -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB_all_2007-08-08.gca transforms/talairach.lta norm.mgz||<|3(bgcolor='#E0E0FF'>norm.mgz||
||<rowbgcolor='#E0E0FF'>nu.mgz||
||<rowbgcolor='#E0E0FF'>transforms/talairach.lta||
||<|3(bgcolor='#FFFFE0'>-[[careg]]||<bgcolor='#E0E0FF'>brainmask.mgz||<|3(bgcolor='#E0E0FF'>[[mri_ca_register]] -align-after -nobigventricles -mask brainmask.mgz -T transforms/talairach.lta norm.mgz $FREESURFER_HOME/average/RB_all_2007-08-08.gca transforms/talairach.m3z||<|3(bgcolor='#E0E0FF'>transforms/talairach.m3z||
||<rowbgcolor='#E0E0FF'>transforms/talairach.lta||
||<rowbgcolor='#E0E0FF'>norm.mgz||
||<|3(bgcolor='#FFFFE0'>-[[careginv]]||<|3(bgcolor='#E0E0FF'>transforms/talairach.m3z||<|3(bgcolor='#E0E0FF'>[[mri_ca_register]] -invert-and-save transforms/talairach.m3z||<bgcolor='#E0E0FF'>transforms/talairach.m3z.inv.x.mgz||
||<rowbgcolor='#E0E0FF'>transforms/talairach.m3z.inv.y.mgz||
||<rowbgcolor='#E0E0FF'>transforms/talairach.m3z.inv.z.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/RB_all_2007-08-08.gca nu_noneck.mgz||<|2(bgcolor='#E0E0FF'>nu_noneck.mgz||
||<rowbgcolor='#E0E0FF'>transforms/talairach.m3z||
||<|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/RB_all_withskull_2007-08-08.gca transforms/talairach_with_skull.lta||<|2(bgcolor='#E0E0FF'>transforms/talairach_with_skull.lta||
||<rowbgcolor='#E0E0FF'>nu_noneck.mgz||
||<|4(bgcolor='#FFFFE0'>-[[calabel]]||<bgcolor='#E0E0FF'>norm.mgz||<|2(bgcolor='#E0E0FF'>[[mri_ca_label]] -align -nobigventricles norm.mgz transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2007-08-08.gca aseg.auto_noCCseg.mgz||<|2(bgcolor='#E0E0FF'>aseg.auto_noCCseg.mgz||
||<rowbgcolor='#E0E0FF'>transforms/talairach.m3z||
||<rowbgcolor='#E0E0FF'>aseg.auto_noCCseg.mgz||<|1(bgcolor='#E0E0FF'>[[mri_cc]] -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz <subjid>||<bgcolor='#E0E0FF'>aseg.auto.mgz||
||<rowbgcolor='#E0E0FF'>aseg.auto.mgz||<bgcolor='#E0E0FF'>cp aseg.auto.mgz aseg.mgz||<bgcolor='#E0E0FF'>aseg.mgz||
||<|3(bgcolor='#FFFFE0'>-[[normalization2]]||<bgcolor='#E0E0FF'>brainmask.mgz||<|3(bgcolor='#E0E0FF'>[[mri_normalize]] -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz||<|3(bgcolor='#E0E0FF'>brain.mgz||
||<rowbgcolor='#E0E0FF'>norm.mgz||
||<rowbgcolor='#E0E0FF'>aseg.mgz||
||<|2(bgcolor='#FFFFE0'>-[[maskbfs]]||<bgcolor='#E0E0FF'>brain.mgz||<|2(bgcolor='#E0E0FF'>[[mri_mask]] -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz||<|2(bgcolor='#E0E0FF'>brain.finalsurfs.mgz||
||<rowbgcolor='#E0E0FF'>brainmask.mgz||
||<|6(bgcolor='#FFFFE0'>-[[segmentation]]||<bgcolor='#E0E0FF'>brain.mgz||<bgcolor='#E0E0FF'>[[mri_segment]] brain.mgz wm.seg.mgz||<bgcolor='#E0E0FF'>wm.seg.mgz||
||<bgcolor='#E0E0FF'>wm.seg.mgz||<|3(bgcolor='#E0E0FF'>[[mri_edit_wm_with_aseg]] wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz||<|3(bgcolor='#E0E0FF'>wm.asegedit.mgz||
||<rowbgcolor='#E0E0FF'>aseg.mgz||
||<rowbgcolor='#E0E0FF'>brain.mgz||
||<bgcolor='#E0E0FF'>wm.asegedit.mgz||<|2(bgcolor='#E0E0FF'>[[mri_pretess]] wm.asegedit.mgz wm norm.mgz wm.mgz||<|2(bgcolor='#E0E0FF'>wm.mgz||
||<rowbgcolor='#E0E0FF'>norm.mgz||
||<|3(bgcolor='#FFFFE0'>-[[fill]]||<bgcolor='#E0E0FF'>wm.mgz||<|3(bgcolor='#E0E0FF'>[[mri_fill]] -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz||<bgcolor='#E0E0FF'>filled.mgz||
||<rowbgcolor='#E0E0FF'>aseg.auto_noCCseg.mgz||<|2(bgcolor='#E0E0FF'>../scripts/ponscc.cut.log||
||<rowbgcolor='#E0E0FF'>transforms/talairach.lta||
||<|8((bgcolor='#FFFFE0'>-[[tessellate]]||<bgcolor='#E0E0FF'>filled.mgz||<|2(bgcolor='#E0E0FF'>[[mri_pretess]] filled.mgz 255 norm.mgz filled-pretess255.mgz||<|2(bgcolor='#E0E0FF'>filled-pretess255.mgz||
||<bgcolor='#E0E0FF'>norm.mgz||
||<bgcolor='#E0E0FF'>filled-pretess255.mgz||<bgcolor='#E0E0FF'>[[mri_tessellate]] filled-pretess255.mgz 255 lh.orig.nofix||<bgcolor='#E0E0FF'>lh.orig.nofix||
||<bgcolor='#E0E0FF'>filled.mgz||<|2(bgcolor='#E0E0FF'>[[mri_pretess]] filled.mgz 127 norm.mgz filled-pretess127.mgz||<|2(bgcolor='#E0E0FF'>filled-pretess127.mgz||
||<bgcolor='#E0E0FF'>norm.mgz||
||<bgcolor='#E0E0FF'>filled-pretess127.mgz||<bgcolor='#E0E0FF'>[[mri_tessellate]] filled-pretess127.mgz 127 rh.orig.nofix||<bgcolor='#E0E0FF'>rh.orig.nofix||
||<bgcolor='#E0E0FF'>?h.orig.nofix||<bgcolor='#E0E0FF'>[[mris_extract_main_component]] ?h.orig.nofix ?h.orig.nofix||<bgcolor='#E0E0FF'>?h.orig.nofix||
||<bgcolor='#E0E0FF'>||<bgcolor='#E0E0FF'>rm -f filled-pretess255.mgz filled-pretess127.mgz||<bgcolor='#E0E0FF'>||
||<bgcolor='#FFFFE0'>-[[smooth|smooth1]]||<bgcolor='#E0E0FF'>?h.orig.nofix||<bgcolor='#E0E0FF'>[[mris_smooth]] -nw ?h.orig.nofix ?h.smoothwm.nofix||<bgcolor='#E0E0FF'>?h.smoothwm.nofix||
||<bgcolor='#FFFFE0'>-[[inflate|inflate1]]||<bgcolor='#E0E0FF'>?h.smoothwm.nofix||<bgcolor='#E0E0FF'>[[mris_inflate]] -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]] -q ?h.inflated.nofix ?h.qsphere.nofix||<bgcolor='#E0E0FF'>?h.qsphere.nofix||
||<|6(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]] -mgz -sphere qsphere.nofix -ga <subjid> ?h||<bgcolor='#E0E0FF'>?h.orig||
||<bgcolor='#E0E0FF'>?h.orig||<bgcolor='#E0E0FF'>[[mris_euler_number]] ?h.orig||<bgcolor='#E0E0FF'>?h.orig||
||<bgcolor='#E0E0FF'>?h.orig||<bgcolor='#E0E0FF'>[[mris_remove_intersection]] ?h.orig ?h.orig||<bgcolor='#E0E0FF'>?h.orig||
||<bgcolor='#E0E0FF'>||<bgcolor='#E0E0FF'>rm ?h.inflated||<bgcolor='#E0E0FF'>||
||<|7(bgcolor='#FFFFE0'>-[[finalsurfs]]||<|3(bgcolor='#E0E0FF'>brain.finalsurfs.mgz||<|7(bgcolor='#E0E0FF'>[[mris_make_surfaces]] -noaparc -mgz -T1 brain.finalsurfs <subjid> ?h||<bgcolor='#E0E0FF'>?h.white||
||<rowbgcolor='#E0E0FF'>?h.pial||
||<rowbgcolor='#E0E0FF'>?h.thickness||
||<|4(rowbgcolor='#E0E0FF'>?h.orig||
||<rowbgcolor='#E0E0FF'>?h.curv||
||<rowbgcolor='#E0E0FF'>?h.area||
||<rowbgcolor='#E0E0FF'>?h.cortex.label||
||<|5(bgcolor='#FFFFE0'>-[[surfvolume]]||<|1(bgcolor='#E0E0FF'>?h.area||<|2(bgcolor='#E0E0FF'>[[mris_calc]] -o ?h.area.mid ?h.area add  ?h.area.pial||<|2(bgcolor='#E0E0FF'>?h.area.mid||
||<rowbgcolor='#E0E0FF'>?h.area.pial||
||<|1(bgcolor='#E0E0FF'>?h.area.mid||<|1(bgcolor='#E0E0FF'>[[mris_calc]] -o ?h.area.mid ?h.area.mid div 2||<bgcolor='#E0E0FF'>?h.area.mid||
||<|1(bgcolor='#E0E0FF'>?h.area.mid||<|2(bgcolor='#E0E0FF'>[[mris_calc]] -o ?h.volume ?h.area.mid mul ?h.thickness||<|2(bgcolor='#E0E0FF'>?h.volume||
||<rowbgcolor='#E0E0FF'>?h.thickness||
||<bgcolor='#FFFFE0'>-[[smooth|smooth2]]||<bgcolor='#E0E0FF'>?h.white||<bgcolor='#E0E0FF'>[[mris_smooth]] -n 3 -nw ?h.white ?h.smoothwm||<bgcolor='#E0E0FF'>?h.smoothwm||
||<|4(bgcolor='#FFFFE0'>-[[inflate|inflate2]]||<|2(bgcolor='#E0E0FF'>?h.smoothwm||<|2(bgcolor='#E0E0FF'>[[mris_inflate]] ?h.smoothwm ?h.inflated||<bgcolor='#E0E0FF'>?h.inflated||
||<(rowbgcolor='#E0E0FF'>?h.sulc||
||<|2(bgcolor='#E0E0FF'>?h.inflated||<|2(bgcolor='#E0E0FF'>[[mris_curvature]] -thresh .999 -n -a 5 -w -distances 10 10 ?h.inflated||<bgcolor='#E0E0FF'>?h.inflated.H||
||<bgcolor='#E0E0FF'>?h.inflated.K||
||<rowbgcolor='#E0E0FF'>||<bgcolor='#E0E0FF'>||<bgcolor='#E0E0FF'>||<bgcolor='#E0E0FF'>||<bgcolor='#E0E0FF'>||
||<|24(bgcolor='#FFFFE0'>'''[[recon-all]] -autorecon3 -subjid <subjid>'''||
||<bgcolor='#FFFFE0'>-[[sphere]]||<bgcolor='#E0E0FF'>?h.inflated,?h.smoothwm||<bgcolor='#E0E0FF'>[[mris_sphere]] ?h.inflated ?h.sphere||<bgcolor='#E0E0FF'>?h.sphere||
||<bgcolor='#FFFFE0'>-[[surfreg]]||<bgcolor='#E0E0FF'>?h.sphere||<bgcolor='#E0E0FF'>[[mris_register]] -curv ?h.sphere $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif ?h.sphere.reg||<bgcolor='#E0E0FF'>?h.sphere.reg||
||<|2(bgcolor='#FFFFE0'>-[[jacobian_white]]||<bgcolor='#E0E0FF'>?h.white||<|2(bgcolor='#E0E0FF'>[[mris_jacobian]] ?h.white ?h.sphere.reg ?h.jacobian_white||<|2(bgcolor='#E0E0FF'>?h.jacobian_white||
||<rowbgcolor='#E0E0FF'>?h.sphere.reg||
||<bgcolor='#FFFFE0'>-[[avgcurv]]||<bgcolor='#E0E0FF'>?h.sphere.reg||<bgcolor='#E0E0FF'>[[mrisp_paint]] -a 5 $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif#6 ?h.sphere.reg ?h.avg_curv||<bgcolor='#E0E0FF'>?h.avg_curv||
||<|2(bgcolor='#FFFFE0'>-[[cortparc]]||<bgcolor='#E0E0FF'>aseg.mgz||<|2(bgcolor='#E0E0FF'>[[mris_ca_label]] -aseg mri/aseg.mgz <subjid> ?h ?h.sphere.reg $FREESURFER_HOME/average/?h.curvature.buckner40.filled.desikan_killiany.2007-06-20gcs ?h.aparc.annot||<|2(bgcolor='#E0E0FF'>label/?h.aparc.annot||
||<rowbgcolor='#E0E0FF'>?h.sphere.reg||
||<bgcolor='#FFFFE0'>-[[parcstats]]||<bgcolor='#E0E0FF'>label/?h.aparc.annot||<bgcolor='#E0E0FF'>[[mris_anatomical_stats]] -mgz -f stats/?h.aparc.stats -b -a label/?h.aparc.annot -c label/aparc.annot.ctab <subjid> ?h||<bgcolor='#E0E0FF'>stats/?h.aparc.stats label/aparc.annot.ctab||
||<|2(bgcolor='#FFFFE0'>-[[cortparc|cortparc2]]||<bgcolor='#E0E0FF'>aseg.mgz||<|2(bgcolor='#E0E0FF'>[[mris_ca_label]] -aseg aseg.mgz <subjid> ?h ?h.sphere.reg $FREESURFER_HOME/average/?h.destrieux.simple.2009-07-29.gcs label/?h.aparc.a2009s.annot||<|2(bgcolor='#E0E0FF'>label/?h.aparc.a2009s.annot||
||<rowbgcolor='#E0E0FF'>?h.sphere.reg||
||<bgcolor='#FFFFE0'>-[[parcstats|parcstats2]]||<bgcolor='#E0E0FF'>label/?h.aparc.a2009s.annot||<bgcolor='#E0E0FF'>[[mris_anatomical_stats]] -mgz -f stats/?h.aparc.a2009s.stats -b -a label/?h.aparc.a2009s.annot -c label/aparc.annot.a2009s.ctab <subjid> ?h||<bgcolor='#E0E0FF'>stats/?h.aparc.a2009s.stats stats/aparc.annot.a2009s.ctab||
||<bgcolor='#FFFFE0'>-[[segstats]]||<bgcolor='#E0E0FF'>aseg.mgz||<bgcolor='#E0E0FF'>[[mri_segstats]] --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --ctab $FREESURFER_HOME/ASegStatsLUT.txt --subject <subjid>||<bgcolor='#E0E0FF'>stats/aseg.stats||
||<|3(bgcolor='#FFFFE0'>-[[cortribbon]]||<bgcolor='#E0E0FF'>aseg.mgz||<|3(bgcolor='#E0E0FF'>[[mris_volmask]] --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance <subjid>||<|3(bgcolor='#E0E0FF'>?h.ribbon.mgz||
||<rowbgcolor='#E0E0FF'>?h.white||
||<rowbgcolor='#E0E0FF'>?h.pial||
||<|6(bgcolor='#FFFFE0'>-[[aparc2aseg]]||<bgcolor='#E0E0FF'> aseg.mgz ||<|3(bgcolor='#E0E0FF'>[[mri_aparc2aseg]] --s <subjid> --ribbon||<|3(bgcolor='#E0E0FF'> aparc+aseg.mgz||
||<rowbgcolor='#E0E0FF'>?h.ribbon.mgz||
||<rowbgcolor='#E0E0FF'>label/?h.aparc.annot||
||<bgcolor='#E0E0FF'> aseg.mgz ||<|3(bgcolor='#E0E0FF'>[[mri_aparc2aseg]] --s <subjid> --ribbon --a2009s||<|3(bgcolor='#E0E0FF'> aparc.a2009s+aseg.mgz||
||<rowbgcolor='#E0E0FF'>?h.ribbon.mgz||
||<rowbgcolor='#E0E0FF'>label/?h.aparc.a2009s.annot||
||<|2(bgcolor='#FFFFE0'>-[[wmparc]]||<bgcolor='#E0E0FF'> aparc+aseg.mgz ||<|1(bgcolor='#E0E0FF'>[[mri_aparc2aseg]] --s <subjid> --labelwm --hypo-as-wm --rip-unknown --ribbon --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz||<|1(bgcolor='#E0E0FF'> wmparc.mgz||
||<bgcolor='#E0E0FF'> wmparc.mgz ||<|1(bgcolor='#E0E0FF'>[[mri_segstats]] --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject <subjid> --surf-wm-vol --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt||<|1(bgcolor='#E0E0FF'> stats/wmparc.stats||
||<rowbgcolor='#E0E0FF'>||<bgcolor='#E0E0FF'>||<bgcolor='#E0E0FF'>||<bgcolor='#E0E0FF'>||<bgcolor='#E0E0FF'>||


=== Differences from Stablev4.0.2 ===
 * mri_cc uses aseg.mgz whereas in v4.0.2, mri_cc uses aseg.auto.mgz.
  * For those using v4.0.2, this means that if edits are made to the aseg.mgz, you must copy the aseg.mgz to aseg.auto.mgz before running -ccseg to generate a new cc segmentation based on your edits.
+||'''recon-all step''' ||'''Individual Flag''' ||'''Input''' ||'''Command Line''' ||'''Output''' ||
||<style="text-align: left;" |18>'''[[recon-all]] -autorecon1 -subjid <subjid>''' ||
||<style="text-align: left;" |2>-i <invol1> -i <invol2> ||invol1.dcm ||[[mri_convert]] invol1.dcm orig/001.mgz ||orig/001.mgz ||
||invol2.dcm ||[[mri_convert]] invol2.dcm orig/002.mgz ||orig/002.mgz ||
||<style="text-align: left;" |4>-[[motioncor]] ||orig/001.mgz ||<style="text-align: left;" |2>[[mri_robust_template]] --mov 001.mgz 002.mgz --average 1 --template rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --subsample 200||<style="text-align: left;" |2>rawavg.mgz ||
||orig/002.mgz ||
||rawavg.mgz ||[[mri_convert]] rawavg.mgz orig.mgz --conform ||orig.mgz ||
||orig.mgz ||[[mri_add_xform_to_header]] -c transforms/talairach.xfm orig.mgz orig.mgz ||orig.mgz ||
||-[[nuintensitycor]] ||orig.mgz ||[[mri_nu_correct.mni]] --i orig.mgz --o nu.mgz --n 2 ||nu.mgz ||
||<style="text-align: left;" |4>-[[talairach]] ||nu.mgz ||[[talairach_avi]] --i nu.mgz --xfm transforms/talairach.auto.xfm ||transforms/talairach.auto.xfm ||
||transforms/talairach.auto.xfm ||cp transforms/talairach.auto.xfm transforms/talairach.xfm ||transforms/talairach.xfm ||
||transforms/talairach.xfm ||[[talairach_afd]] -T 0.005 -xfm transforms/talairach.xfm ||transforms/talairach.xfm ||
|| ||awk -f $FREESURFER_HOME/bin/extract_talairach_avi_QA.awk transforms/talairach_avi.log ||transforms/talairach_avi.log ||
||-[[normalization]] ||nu.mgz ||[[mri_normalize]] -g 1 nu.mgz T1.mgz ||T1.mgz ||
||<style="text-align: left;" |5>-[[skullstrip]] ||nu.mgz ||[[mri_em_register]] -skull nu.mgz $FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta ||transforms/talairach_with_skull.lta ||
||T1.mgz ||[[mri_watershed]] -T1 -brain_atlas $FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz ||brainmask.auto.mgz ||
||T1.mgz||<style="text-align: left;"|2>mri_gcut -110 -mult brainmask.auto.mgz T1.mgz brainmask.auto.mgz ||<style="text-align: left;"|2>brainmask.auto.mgz||
||brainmask.auto.mgz||
||brainmask.auto.mgz ||cp brainmask.auto.mgz brainmask.mgz ||brainmask.mgz ||
|| || || || || ||
||<style="text-align: left;" |66>'''[[recon-all]] -autorecon2 -subjid <subjid>''' ||
||<style="text-align: left;" |2>-[[gcareg]] ||brainmask.mgz ||<style="text-align: left;" |2>[[mri_em_register]] -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB_all_2008-03-26.gca transforms/talairach.lta ||<style="text-align: left;" |2>transforms/talairach.lta ||
||nu.mgz ||
||<style="text-align: left;" |3>-[[canorm]] ||brainmask.mgz ||<style="text-align: left;" |3>[[mri_ca_normalize]] -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz ||<style="text-align: left;" |3>norm.mgz ||
||nu.mgz ||
||transforms/talairach.lta ||
||<style="text-align: left;" |3>-[[careg]] ||brainmask.mgz ||<style="text-align: left;" |3>[[mri_ca_register]] -align-after -nobigventricles -mask brainmask.mgz -T transforms/talairach.lta norm.mgz $FREESURFER_HOME/average/RB_all_2008-03-26.gca transforms/talairach.m3z ||<style="text-align: left;" |3>transforms/talairach.m3z ||
||transforms/talairach.lta ||
||norm.mgz ||
||<style="text-align: left;" |3>-[[careginv]] ||<style="text-align: left;" |3>transforms/talairach.m3z ||<style="text-align: left;" |3>[[mri_ca_register]] -invert-and-save transforms/talairach.m3z ||transforms/talairach.m3z.inv.x.mgz ||
||transforms/talairach.m3z.inv.y.mgz ||
||transforms/talairach.m3z.inv.z.mgz ||
||<style="text-align: left;" |2>-[[rmneck]] ||nu.mgz ||<style="text-align: left;" |2>[[mri_remove_neck]] -radius 25 nu.mgz transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2008-03-26.gca nu_noneck.mgz ||<style="text-align: left;" |2>nu_noneck.mgz ||
||transforms/talairach.m3z ||
||<style="text-align: left;" |2>-[[skull-lta]] ||transforms/talairach.lta ||<style="text-align: left;" |2>[[mri_em_register]] -skull -t transforms/talairach.lta nu_noneck.mgz $FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta ||<style="text-align: left;" |2>transforms/talairach_with_skull.lta ||
||nu_noneck.mgz ||
||<style="text-align: left;" |4>-[[calabel]] ||norm.mgz ||<style="text-align: left;" |2>[[mri_ca_label]] -align -nobigventricles norm.mgz transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz ||<style="text-align: left;" |2>aseg.auto_noCCseg.mgz ||
||transforms/talairach.m3z ||
||aseg.auto_noCCseg.mgz ||<style="text-align: left;" |1>[[mri_cc]] -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz <subjid> ||aseg.auto.mgz ||
||aseg.auto.mgz ||cp aseg.auto.mgz aseg.mgz ||aseg.mgz ||
||<style="text-align: left;" |3>-[[normalization2]] ||brainmask.mgz ||<style="text-align: left;" |3>[[mri_normalize]] -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz ||<style="text-align: left;" |3>brain.mgz ||
||norm.mgz ||
||aseg.mgz ||
||<style="text-align: left;" |2>-[[maskbfs]] ||brain.mgz ||<style="text-align: left;" |2>[[mri_mask]] -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz ||<style="text-align: left;" |2>brain.finalsurfs.mgz ||
||brainmask.mgz ||
||<style="text-align: left;" |6>-[[segmentation]] ||brain.mgz ||[[mri_segment]] brain.mgz wm.seg.mgz ||wm.seg.mgz ||
||wm.seg.mgz ||<style="text-align: left;" |3>[[mri_edit_wm_with_aseg]] wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz ||<style="text-align: left;" |3>wm.asegedit.mgz ||
||aseg.mgz ||
||brain.mgz ||
||wm.asegedit.mgz ||<style="text-align: left;" |2>[[mri_pretess]] wm.asegedit.mgz wm norm.mgz wm.mgz ||<style="text-align: left;" |2>wm.mgz ||
||norm.mgz ||
||<style="text-align: left;" |3>-[[fill]] ||wm.mgz ||<style="text-align: left;" |3>[[mri_fill]] -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz ||filled.mgz ||
||aseg.auto_noCCseg.mgz ||<style="text-align: left;" |2>../scripts/ponscc.cut.log ||
||transforms/talairach.lta ||
||<style="text-align: left;" |8>-[[tessellate]] ||filled.mgz ||<style="text-align: left;" |2>[[mri_pretess]] filled.mgz 255 norm.mgz filled-pretess255.mgz ||<style="text-align: left;" |2>filled-pretess255.mgz ||
||norm.mgz ||
||filled-pretess255.mgz ||[[mri_tessellate]] filled-pretess255.mgz 255 lh.orig.nofix ||lh.orig.nofix ||
||filled.mgz ||<style="text-align: left;" |2>[[mri_pretess]] filled.mgz 127 norm.mgz filled-pretess127.mgz ||<style="text-align: left;" |2>filled-pretess127.mgz ||
||norm.mgz ||
||filled-pretess127.mgz ||[[mri_tessellate]] filled-pretess127.mgz 127 rh.orig.nofix ||rh.orig.nofix ||
||?h.orig.nofix ||[[mris_extract_main_component]] ?h.orig.nofix ?h.orig.nofix ||?h.orig.nofix ||
|| ||rm -f filled-pretess255.mgz filled-pretess127.mgz || ||
||-[[smooth|smooth1]] ||?h.orig.nofix ||[[mris_smooth]] -nw ?h.orig.nofix ?h.smoothwm.nofix ||?h.smoothwm.nofix ||
||-[[inflate|inflate1]] ||?h.smoothwm.nofix ||[[mris_inflate]] -no-save-sulc ?h.smoothwm.nofix ?h.inflated.nofix ||?h.inflated.nofix ||
||-[[qsphere]] ||?h.inflated.nofix ||[[mris_sphere]] -q ?h.inflated.nofix ?h.qsphere.nofix ||?h.qsphere.nofix ||
||<style="text-align: left;" |6>-[[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]] -mgz -sphere qsphere.nofix -ga <subjid> ?h ||?h.orig ||
||?h.orig ||[[mris_euler_number]] ?h.orig ||?h.orig ||
||?h.orig ||[[mris_remove_intersection]] ?h.orig ?h.orig ||?h.orig ||
|| ||rm ?h.inflated || ||
||<style="text-align: left;" |5>-white ||<style="text-align: left;" |1>aseg.mgz, brain.finalsurfs.mgz, wm.mgz, filled.mgz ||<style="text-align: left;" |5>[[mris_make_surfaces]] -whiteonly -noaparc -mgz -T1 brain.finalsurfs <subjid> ?h ||?h.white ||
||<style="text-align: left;" |4>?h.orig ||
||?h.curv ||
||?h.area||
||?h.cortex.label ||
||<style="text-align: left;" |5>-[[surfvolume]] ||<style="text-align: left;" |1>?h.area ||<style="text-align: left;" |2>[[mris_calc]] -o ?h.area.mid ?h.area add  ?h.area.pial ||<style="text-align: left;" |2>?h.area.mid ||
||?h.area.pial ||
||<style="text-align: left;" |1>?h.area.mid ||<style="text-align: left;" |1>[[mris_calc]] -o ?h.area.mid ?h.area.mid div 2 ||?h.area.mid ||
||<style="text-align: left;" |1>?h.area.mid ||<style="text-align: left;" |2>[[mris_calc]] -o ?h.volume ?h.area.mid mul ?h.thickness ||<style="text-align: left;" |2>?h.volume ||
||?h.thickness ||
||-[[smooth|smooth2]] ||?h.white ||[[mris_smooth]] -n 3 -nw ?h.white ?h.smoothwm ||?h.smoothwm ||
||<style="text-align: left;" |4>-[[inflate|inflate2]] ||<style="text-align: left;" |2>?h.smoothwm ||<style="text-align: left;" |2>[[mris_inflate]] ?h.smoothwm ?h.inflated ||?h.inflated ||
||<style="text-align: left;">?h.sulc ||
||<style="text-align: left;" |2>?h.inflated ||<style="text-align: left;" |2>[[mris_curvature]] -thresh .999 -n -a 5 -w -distances 10 10 ?h.inflated ||?h.inflated.H ||
||?h.inflated.K ||
|| || || || || ||
||<style="text-align: left;" |26>'''[[recon-all]] -autorecon3 -subjid <subjid>''' ||
||-[[sphere]] ||?h.inflated,?h.smoothwm ||[[mris_sphere]] ?h.inflated ?h.sphere ||?h.sphere ||
||-[[surfreg]] ||?h.sphere ||[[mris_register]] -curv ?h.sphere $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif ?h.sphere.reg ||?h.sphere.reg ||
||<style="text-align: left;" |2>-[[jacobian_white]] ||?h.white ||<style="text-align: left;" |2>[[mris_jacobian]] ?h.white ?h.sphere.reg ?h.jacobian_white ||<style="text-align: left;" |2>?h.jacobian_white ||
||?h.sphere.reg ||
||-[[avgcurv]] ||?h.sphere.reg ||[[mrisp_paint]] -a 5 $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif#6 ?h.sphere.reg ?h.avg_curv ||?h.avg_curv ||
||<style="text-align: left;" |2>-[[cortparc]] ||aseg.mgz ||<style="text-align: left;" |2>[[mris_ca_label]] -aseg mri/aseg.mgz <subjid> ?h ?h.sphere.reg $FREESURFER_HOME/average/?h.curvature.buckner40.filled.desikan_killiany.2007-06-20gcs ?h.aparc.annot ||<style="text-align: left;" |2>label/?h.aparc.annot ||
||?h.sphere.reg ||
||-[[parcstats]] ||label/?h.aparc.annot ||[[mris_anatomical_stats]] -mgz -f stats/?h.aparc.stats -b -a label/?h.aparc.annot -c label/aparc.annot.ctab <subjid> ?h ||stats/?h.aparc.stats label/aparc.annot.ctab ||
||<style="text-align: left;" |2>-[[cortparc|cortparc2]] ||aseg.mgz ||<style="text-align: left;" |2>[[mris_ca_label]] -aseg aseg.mgz <subjid> ?h ?h.sphere.reg $FREESURFER_HOME/average/?h.destrieux.simple.2009-07-29.gcs label/?h.aparc.a2009s.annot ||<style="text-align: left;" |2>label/?h.aparc.a2009s.annot ||
||?h.sphere.reg ||
||-[[parcstats|parcstats2]] ||label/?h.aparc.a2009s.annot ||[[mris_anatomical_stats]] -mgz -f stats/?h.aparc.a2009s.stats -b -a label/?h.aparc.a2009s.annot -c label/aparc.annot.a2009s.ctab <subjid> ?h ||stats/?h.aparc.a2009s.stats stats/aparc.annot.a2009s.ctab ||
||<style="text-align: left;" |3>-[[cortribbon]] ||aseg.mgz ||<style="text-align: left;" |3>[[mris_volmask]] --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance <subjid> ||<style="text-align: left;" |3>?h.ribbon.mgz ||
||?h.white ||
||?h.pial ||
||-[[segstats]] ||aseg.mgz ||[[mri_segstats]] --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --totalgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --ctab $FREESURFER_HOME/ASegStatsLUT.txt --subject <subjid>||stats/aseg.stats ||
||<style="text-align: left;" |6>-[[aparc2aseg]] ||aseg.mgz ||<style="text-align: left;" |3>[[mri_aparc2aseg]] --s <subjid> --ribbon ||<style="text-align: left;" |3>aparc+aseg.mgz ||
||?h.ribbon.mgz ||
||label/?h.aparc.annot ||
||aseg.mgz ||<style="text-align: left;" |3>[[mri_aparc2aseg]] --s <subjid> --ribbon --a2009s ||<style="text-align: left;" |3>aparc.a2009s+aseg.mgz ||
||?h.ribbon.mgz ||
||label/?h.aparc.a2009s.annot ||
||<style="text-align: left;" |2>-[[wmparc]] ||aparc+aseg.mgz ||<style="text-align: left;" |1>[[mri_aparc2aseg]] --s <subjid> --labelwm --hypo-as-wm --rip-unknown --ribbon --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz ||<style="text-align: left;" |1>wmparc.mgz ||
||wmparc.mgz ||<style="text-align: left;" |1>[[mri_segstats]] --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject <subjid> --surf-wm-vol --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt ||<style="text-align: left;" |1>stats/wmparc.stats ||
||-[[BrodmannAreaMaps|balabels]] ||?h.sphere.reg ||[[mri_label2label]] --srcsubject fsaverage --srclabel fsaverage/label/?h.BA*.label --trgsubject <subjid> --trglabel ?h.BA*.label --hemi ?h --regmethod surface|| label/?h.BA*.label||
||-label-exvivo-ec ||?h.sphere.reg ||[[mris_spherical_average]] -erode 1 -orig white -t 0.4 -o <subjid> label ?h.entorhinal ?h sphere.reg ?h.EC_average ?h.entorhinal_exvivo.label|| label/?h.entorhinal_exvivo.label||
||||||||||<style="text-align: center;"> ||