Diff for "ReconAllDevTable" - Free Surfer Wiki

Differences between revisions 1 and 231 (spanning 230 versions)

FreeSurfer Tutorial: Process Flow

This table shows the recon-all steps for the current dev version of FreeSurfer. Updated Nov 2014 NJS

See ReconAllTableStableV5.1 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>	invol1.dcm or .nii or .mgz	mri_convert invol1.dcm orig/001.mgz	orig/001.mgz
	-i <invol2> optional	invol2.dcm or .nii or .mgz	mri_convert invol2.dcm orig/002.mgz	orig/002.mgz
	-T2 <invol> or -FLAIR <invol> optional	invol.dcm or .nii or .mgz	mri_convert --no_scale 1 invol.dcm orig/T2raw.mgz	orig/T2raw.mgz
	-motioncor	orig/001.mgz	mri_robust_template --mov 001.mgz 002.mgz --average 1 --template rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout --subsample 200 --lta	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
	-talairach	orig.mgz	mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz	orig_nu.mgz
		orig_nu.mgz	talairach_avi --i orig_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	orig_nu.mgz	mri_normalize -g 1 orig_nu.mgz T1.mgz	T1.mgz
	-skullstrip	orig_nu.mgz	mri_em_register -skull orig_nu.mgz $FREESURFER_HOME/average/RB_all_withskull_2014-08-21.gca transforms/talairach_with_skull.lta	transforms/talairach_with_skull.lta
		T1.mgz	mri_watershed -T1 -brain_atlas $FREESURFER_HOME/average/RB_all_withskull_2014-08-21.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz	brainmask.auto.mgz
		brainmask.auto.mgz	cp brainmask.auto.mgz brainmask.mgz	brainmask.mgz

recon-all step	Individual Flag	Input	Command Line	Output
recon-all -autorecon2 -subjid <subjid>
	-nuintensitycor	orig.mgz	mri_nu_correct.mni --i orig.mgz --mask brainmask.mgz --o nu.mgz --n 1 --proto-iters 1000 --uchar transforms/talairach.xfm	nu.mgz
		brainmask.mgz
		talairach.xfm
	-gcareg	brainmask.mgz	mri_em_register -uns 3 -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB_all_2014-08-21.gca transforms/talairach.lta	transforms/talairach.lta
		nu.mgz
	-canorm	brainmask.mgz	mri_ca_normalize -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB_all_2014-08-21.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_2014-08-21.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_2014-08-21.gca nu_noneck.mgz	nu_noneck.mgz
		transforms/talairach.m3z
	-skull-lta	transforms/talairach.lta	mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz $FREESURFER_HOME/average/RB_all_withskull_2014-08-21.gca transforms/talairach_with_skull_2.lta	transforms/talairach_with_skull_2.lta
		nu_noneck.mgz
	-calabel	norm.mgz	mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2014-08-21.gca aseg.auto_noCCseg.mgz	aseg.auto_noCCseg.mgz
		transforms/talairach.m3z
		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.presurf.mgz	aseg.presurf.mgz
	-normalization2	brainmask.mgz	mri_normalize -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz	brain.mgz
		norm.mgz
		aseg.presurf.mgz
	-maskbfs	brain.mgz	mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz	brain.finalsurfs.mgz
		brainmask.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.presurf.mgz wm.asegedit.mgz	wm.asegedit.mgz
		aseg.presurf.mgz
		brain.mgz
		wm.asegedit.mgz	mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz	wm.mgz
		norm.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
	-tessellate	filled.mgz	mri_pretess filled.mgz 255 norm.mgz filled-pretess255.mgz	filled-pretess255.mgz
		norm.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
		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.presurf.mgz	mris_make_surfaces -whiteonly -noaparc -mgz -T1 brain.finalsurfs <subjid> ?h	?h.white
		brain.finalsurfs.mgz
		wm.mgz
		filled.mgz
		?h.orig
				?h.curv
				?h.area
				?h.cortex.label
	-smooth2	?h.white	mris_smooth -n 3 -nw ?h.white ?h.smoothwm	?h.smoothwm
	-inflate2	?h.smoothwm	mris_inflate ?h.smoothwm.nofix ?h.inflated	?h.inflated
?h.sulc
-curvHK	?h.white	mris_curvature -w ?h.white	?h.white.H
			?h.white.K
	?h.inflated	mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ?h.inflated	?h.inflated.H
			?h.inflated.K
-curvstats	?h.smoothwm	mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/?h.curv.stats -F smoothwm <subjid> ?h curv sulc	stats/?h.curv.stats
	?h.curv
	?h.sulc

recon-all step	Individual Flag	Input	Command Line	Output
recon-all -autorecon3 -subjid <subjid>
	-sphere	?h.inflated	mris_sphere ?h.inflated ?h.sphere	?h.sphere
		?h.smoothwm
	-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
		?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
	-cortparc	aseg.presurf.mgz	mris_ca_label -l ../label/lh.cortex.label -aseg mri/aseg.presurf.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
		?h.cortex.label
		?h.sphere.reg
	-pial	aseg.presurf.mgz	mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs <subjid> ?h	?h.pial
		brain.finalsurfs.mgz
		wm.mgz
		filled.mgz
		?h.orig
				?h.curv.pial
				?h.area.pial
		label/?h.aparc.annot		?h.thickness
	-T2pial or -FLAIRpial optional	x	y	z
	-surfvolume	?h.area	mris_calc -o ?h.area.mid ?h.area add ?h.area.pial	?h.area.mid
		?h.area.pial
		?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
	-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.presurf.mgz	mris_ca_label -l ../label/lh.cortex.label -aseg aseg.presurf.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
		?h.sphere.reg
		label/?h.cortex.label
	-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
	-cortparc3	aseg.presurf.mgz	mris_ca_label ../label/lh.cortex.label -aseg aseg.presurf.mgz <subjid> ?h ?h.sphere.reg $FREESURFER_HOME/average/?h.DKTatlas40.gcs ../label/?h.aparc.DKTatlas40.annot	label/?h.aparc.a2009s.annot
		?h.sphere.reg
		label/?h.cortex.label
	-parcstats3	label/?h.aparc.a2009s.annot	mris_anatomical_stats -mgz -f stats/?h.aparc.DKTatlas.stats -b -a label/?h.aparc.DKTatlas.annot -c label/aparc.annot.DKTatlas.ctab <subjid> ?h	stats/?h.aparc.a2009s.stats
				stats/aparc.annot.a2009s.ctab
	-pctsurfcon	rawavg.mgz	pctsurfcon --s <subjid> --?h-only	?h.w-g.pct.mgh
		orig.mgz
		?h.cortex.label		stats/?h.w-g.pct.stats
		?h.white
	-cortribbon	aseg.presurf.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		ribbon.mgz
	-hyporelabel	aseg.presurf.mgz	mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz	aseg.presurf.hypos.mgz
		?h.white
	-aparc2aseg	aseg.presurf.hypos.mgz	mri_aparc2aseg --s <subjid> --ribbon	aparc+aseg.mgz
		?h.ribbon.mgz
		label/?h.aparc.annot
		ribbon.mgz
		aseg.presurf.hypos.mgz	mri_aparc2aseg --s <subjid> --ribbon --a2009s	aparc.a2009s+aseg.mgz
		?h.ribbon.mgz
		label/?h.aparc.a2009s.annot
		ribbon.mgz
	-apas2aseg	aparc+aseg.mgz	apas2aseg --i aparc+aseg.mgz --o aseg.mgz	aseg.mgz
	-segstats	aseg.mgz	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 --totalgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab $FREESURFER_HOME/ASegStatsLUT.txt --subject <subjid>	stats/aseg.stats
		norm.mgz
	-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.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 --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 1 as of 2006-01-09 17:58:32 → 
  Size: 7565
  Editor: JenniPacheco
  Comment:
+   ← Revision 231 as of 2014-11-06 14:42:12 → ⇥
  Size: 18168
  Editor: NickSchmansky
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
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+#acl LcnGroup:read,write,delete,revert All:read
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+This table shows the recon-all steps for the current '''dev''' version of FreeSurfer.   ''Updated Nov 2014 NJS''

See [[ReconAllTableStableV5.1]] to see a process flow for the latest '''stable''' version of FreeSurfer.

Click [[ReconAllBlockDiagram|here]] to see this information presented in a block diagram format and [[ReconAllFilesVsSteps|here for a process v. files table]].

See also the OtherUsefulFlags for other recon-all options.
||<tablealign="left" tablestyle="text-align:left">'''recon-all step''' ||'''Individual Flag''' ||'''Input''' ||'''Command Line''' ||'''Output''' ||
||<style="text-align:left;" |17>>'''[[recon-all]] -autorecon1 -subjid <subjid>''' ||
||<style="text-align:left;" |1>-i <invol1> ||invol1.dcm ''or .nii or .mgz'' ||[[mri_convert]] invol1.dcm orig/001.mgz ||orig/001.mgz ||
||<style="text-align:left" |1>-i <invol2> ''optional'' ||invol2.dcm'' or .nii or .mgz'' ||[[mri_convert]] invol2.dcm orig/002.mgz ||orig/002.mgz ||
||<style="text-align:left" |1>-T2 <invol> ''or'' <<BR>> -FLAIR <invol> ''optional'' ||<style="text-align:left" |1>invol.dcm ''or .nii or .mgz'' ||<style="text-align:left" |1>[[mri_convert]] --no_scale 1 invol.dcm orig/T2raw.mgz ||<style="text-align:left" |1>orig/T2raw.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 --iscaleout --subsample 200 --lta ||<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 ||
||<style="text-align:left;" |5>-[[talairach]] ||orig.mgz ||[[mri_nu_correct.mni]] --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz ||orig_nu.mgz ||
||orig_nu.mgz ||[[talairach_avi]] --i orig_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]] ||orig_nu.mgz ||[[mri_normalize]] -g 1 orig_nu.mgz T1.mgz ||T1.mgz ||
||<style="text-align:left;" |3>-[[skullstrip]] ||orig_nu.mgz ||[[mri_em_register]] -skull orig_nu.mgz $FREESURFER_HOME/average/RB_all_withskull_2014-08-21.gca transforms/talairach_with_skull.lta ||transforms/talairach_with_skull.lta ||
||T1.mgz ||[[mri_watershed]] -T1 -brain_atlas $FREESURFER_HOME/average/RB_all_withskull_2014-08-21.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz ||brainmask.auto.mgz ||
||brainmask.auto.mgz ||cp brainmask.auto.mgz brainmask.mgz ||brainmask.mgz ||
-Line 4:
+Line 30:
-||<rowbgcolor='#80FF80'>'''recon-all step'''||'''Individual Flag'''||'''Input'''||'''Command Line'''||'''Output'''||
||<bgcolor='#FFFFE0'>none||<bgcolor='#FFFFE0'>none||<bgcolor='#E0E0FF'>file.dcm||<bgcolor='#E0E0FF'>["mri_convert"] file.dcm orig/001.mgz||<bgcolor='#E0E0FF'>orig/001.mgz||
||<|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||
||<rowbgcolor='#E0E0FF'>orig/002.mgz||
||<rowbgcolor='#E0E0FF'>rawavg.mgz||["mri_convert"] rawavg.mgz orig.mgz --conform||orig.mgz||
||<|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'>-talairach||<bgcolor='#E0E0FF'>nu.mgz||<bgcolor='#E0E0FF'>["talairach2"] subjid -mgz||<bgcolor='#E0E0FF'>transforms/talairach.xfm||
||<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||
||<-5(rowbgcolor='#FF8080'>Check skullstrip (brain.mgz), talairach (transforms/talairach.xfm), and normalization (brain.mgz or T1.mgz - mean wm voxel value = 110)||
||<|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||
||<rowbgcolor='#E0E0FF'>nu.mgz||
||<|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||
||<rowbgcolor='#E0E0FF'>nu.mgz||
||<rowbgcolor='#E0E0FF'>transforms/talairach.lta||
||<|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||
||<rowbgcolor='#E0E0FF'>transforms/talairach.lta||
||<rowbgcolor='#E0E0FF'>norm.mgz||
||<|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||
||<rowbgcolor='#E0E0FF'>transforms/talairach.m3z||
||<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||
||<bgcolor='#FFFFE0'>-segmentation||<bgcolor='#E0E0FF'>brain.mgz||<bgcolor='#E0E0FF'>["mri_segment"] brain.mgz wm.mgz||<bgcolor='#E0E0FF'>wm.mgz||
||<|2(bgcolor='#FFFFE0'>-edit_wm_with_aseg||<bgcolor='#E0E0FF'>wm.mgz||<|2(bgcolor='#E0E0FF'>["mri_edit_wm_with_aseg"] wm.mgz aseg.mgz wm.mgz||<|2(bgcolor='#E0E0FF'>wm.mgz||
||<rowbgcolor='#E0E0FF'>aseg.mgz||
||<|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||
||<bgcolor='#FFFFE0'>-euler||<bgcolor='#E0E0FF'>?h.orig||<bgcolor='#E0E0FF'>["mris_euler_number"] ?h.orig||<bgcolor='#E0E0FF'>?h.orig.euler||
||<bgcolor='#FFFFE0'>-smooth2||<bgcolor='#E0E0FF'>?h.orig||<bgcolor='#E0E0FF'>["mris_smooth"] ?h.orig ?h.smoothwm||<bgcolor='#E0E0FF'>?h.smoothwm||
||<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||
||<rowbgcolor='#E0E0FF'>?h.thickness||
||<|3(bgcolor='#FFFFE0'>-cortribbon||<bgcolor='#E0E0FF'>orig.mgz||<|3(bgcolor='#E0E0FF'>["mri_surf2vol"] --mkmask --hemi ?h --fillribbon --template orig.mgz --volregidentity subj --outvol ?h.ribbon.mgz||<|3(bgcolor='#E0E0FF'>?h.ribbon.mgz||
||<rowbgcolor='#E0E0FF'>?h.white||
||<rowbgcolor='#E0E0FF'>?h.pial||
||<-5(rowbgcolor='#FF8080'>Check final surfaces '''tkmedit subj wm.mgz ?h.white brain.mgz'''||
||<|8(bgcolor='#FFFFE0'>["recon-all"] -autorecon3 -subjid subj||
||<bgcolor='#FFFFE0'>-sphere||<bgcolor='#E0E0FF'>?h.inflated||<bgcolor='#E0E0FF'>["mris_sphere"] -w 0 ?h.inflated ?h.sphere||<bgcolor='#E0E0FF'>?h.sphere||
||<bgcolor='#FFFFE0'>-surfreg||<bgcolor='#E0E0FF'>?h.sphere||<bgcolor='#E0E0FF'>["mris_register"] -w 0 -curv ?h.sphere $AvgTif ?h.sphere.reg||<bgcolor='#E0E0FF'>?h.sphere.reg||
||<|2(bgcolor='#FFFFE0'>-contrasurfreg||<bgcolor='#E0E0FF'>rh.sphere||<bgcolor='#E0E0FF'>["mris_register"] -w 0 -curv -reverse rh.sphere $AvgTif rh.lh.sphere.reg||<bgcolor='#E0E0FF'>rh.lh.sphere.reg||
||<rowbgcolor='#E0E0FF'>lh.sphere||["mris_register"] -w 0 -curv -reverse lh.sphere $AvgTif lh.rh.sphere.reg||lh.rh.sphere.reg||
||<bgcolor='#FFFFE0'>-avgcurv||<bgcolor='#E0E0FF'>?h.sphere.reg||<bgcolor='#E0E0FF'>["mrisp_paint"] -a 5 $AvgTif#6 ?h.sphere.reg ?h.avg_curv||<bgcolor='#E0E0FF'>?h.avg_curv||
||<bgcolor='#FFFFE0'>-cortparc||<bgcolor='#E0E0FF'>?h.sphere.reg||<bgcolor='#E0E0FF'>["mris_ca_label"] -t $CPAnnotTable subj ?h sphere.reg $CPAtlas ?h.aparc.annot||<bgcolor='#E0E0FF'>label/?h.aparc.annot||
||<bgcolor='#FFFFE0'>-parcstats||<bgcolor='#E0E0FF'>label/?h.aparc.annot||<bgcolor='#E0E0FF'>["mris_anatomical_stats"] -f scripts/?h.aparc.stats -b -a label/?h.aparc.annot subj ?h||<bgcolor='#E0E0FF'>stats/?h.aparc.stats||
+||<tablealign="left" tablestyle="text-align:left">'''recon-all step''' ||'''Individual Flag''' ||'''Input''' ||'''Command Line''' ||'''Output''' ||
||<style="text-align:left;" |72>'''[[recon-all]] -autorecon2 -subjid <subjid>''' ||
||<style="text-align:left;" |3>-[[nuintensitycor]] ||orig.mgz ||<style="text-align:left;" |3>[[mri_nu_correct.mni]] --i orig.mgz --mask brainmask.mgz --o nu.mgz --n 1 --proto-iters 1000 --uchar transforms/talairach.xfm ||<style="text-align:left;" |3>nu.mgz ||
||brainmask.mgz ||
||talairach.xfm ||
||<style="text-align:left;" |2>-[[gcareg]] ||brainmask.mgz ||<style="text-align:left;" |2>[[mri_em_register]] -uns 3 -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB_all_2014-08-21.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_2014-08-21.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_2014-08-21.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_2014-08-21.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_2014-08-21.gca transforms/talairach_with_skull_2.lta ||<style="text-align:left;" |2>transforms/talairach_with_skull_2.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_2014-08-21.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.presurf.mgz ||aseg.presurf.mgz ||
||<style="text-align:left;" |3>-[[normalization2]] ||brainmask.mgz ||<style="text-align:left;" |3>[[mri_normalize]] -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz ||<style="text-align:left;" |3>brain.mgz ||
||norm.mgz ||
||aseg.presurf.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.presurf.mgz wm.asegedit.mgz ||<style="text-align:left;" |3>wm.asegedit.mgz ||
||aseg.presurf.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;" |8>-white ||<style="text-align:left;" |1>aseg.presurf.mgz ||<style="text-align:left;" |8>[[mris_make_surfaces]] -whiteonly -noaparc -mgz -T1 brain.finalsurfs <subjid> ?h ||<style="text-align:left" |4>?h.white ||
||<style="text-align:left">brain.finalsurfs.mgz ||
||<style="text-align:left">wm.mgz ||
||<style="text-align:left">filled.mgz ||
||<style="text-align:left;" |4>?h.orig ||
||?h.curv ||
||?h.area ||
||?h.cortex.label ||
||-[[smooth|smooth2]] ||?h.white ||[[mris_smooth]] -n 3 -nw ?h.white ?h.smoothwm ||?h.smoothwm ||
||<style="text-align:left" |2>-[[inflate|inflate2]] ||<style="text-align:left" |2>?h.smoothwm ||<style="text-align:left" |2>[[mris_inflate]] ?h.smoothwm.nofix ?h.inflated ||?h.inflated ||
||?h.sulc ||
||<style="text-align:left" |4>-curvHK ||<style="text-align:left" |2>?h.white ||<style="text-align:left" |2>[[mris_curvature]] -w ?h.white ||<style="text-align:left" |1>?h.white.H ||
||?h.white.K ||
||<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 ||<style="text-align:left" |1>?h.inflated.H ||
||?h.inflated.K ||
||<style="text-align:left" |3>-curvstats ||<style="text-align:left">?h.smoothwm ||<style="text-align:left" |3>mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/?h.curv.stats -F smoothwm <subjid> ?h curv sulc ||<style="text-align:left" |3>stats/?h.curv.stats ||
||<style="text-align:left">?h.curv ||
||<style="text-align:left">?h.sulc ||
-Line 64:
+Line 105:
-Click here to see a table of OtherUsefulFlags
+||<tablealign="left" tablestyle="text-align:left">'''recon-all step''' ||'''Individual Flag''' ||'''Input''' ||'''Command Line''' ||'''Output''' ||
||<style="text-align:left;" |64>'''[[recon-all]] -autorecon3 -subjid <subjid>''' ||
||<style="text-align:left" |2>-[[sphere]] ||?h.inflated ||<style="text-align:left" |2>[[mris_sphere]] ?h.inflated ?h.sphere ||<style="text-align:left" |2>?h.sphere ||
||<style="text-align:left">?h.smoothwm ||
||-[[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;" |3>-[[cortparc]] ||aseg.presurf.mgz ||<style="text-align:left;" |3>[[mris_ca_label]] -l ../label/lh.cortex.label -aseg mri/aseg.presurf.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;" |3>label/?h.aparc.annot ||
||<style="text-align:left">?h.cortex.label ||
||?h.sphere.reg ||
||<style="text-align:left;" |8>-pial ||<style="text-align:left;" |1>aseg.presurf.mgz ||<style="text-align:left;" |8>[[mris_make_surfaces]] -white NOWRITE -mgz -T1 brain.finalsurfs <subjid> ?h ||<style="text-align:left" |4>?h.pial ||
||brain.finalsurfs.mgz ||
||wm.mgz ||
||filled.mgz ||
||<style="text-align:left;" |3>?h.orig ||
||?h.curv.pial ||
||<style="text-align:left">?h.area.pial ||
||<style="text-align:left" |1>label/?h.aparc.annot ||?h.thickness ||
||<style="text-align:left" |1>-T2pial ''or'' <<BR>> -FLAIRpial ''optional'' ||x ||<style="text-align:left |1">y ||<style="text-align:left" |1>z ||
||<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 ||
||<style="text-align:left" |2>-[[parcstats]] ||<style="text-align:left" |2>label/?h.aparc.annot ||<style="text-align:left" |2>[[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;" |3>-[[cortparc|cortparc2]] ||aseg.presurf.mgz ||<style="text-align:left;" |3>[[mris_ca_label]] -l ../label/lh.cortex.label -aseg aseg.presurf.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;" |3>label/?h.aparc.a2009s.annot ||
||?h.sphere.reg ||
||label/?h.cortex.label ||
||<style="text-align:left" |2>-[[parcstats|parcstats2]] ||<style="text-align:left" |2>label/?h.aparc.a2009s.annot ||<style="text-align:left" |2>[[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>-[[cortparc|cortparc3]] ||aseg.presurf.mgz ||<style="text-align:left;" |3>[[mris_ca_label]]  ../label/lh.cortex.label -aseg aseg.presurf.mgz <subjid> ?h ?h.sphere.reg $FREESURFER_HOME/average/?h.DKTatlas40.gcs ../label/?h.aparc.DKTatlas40.annot ||<style="text-align:left;" |3>label/?h.aparc.a2009s.annot ||
||?h.sphere.reg ||
||label/?h.cortex.label ||
||<style="text-align:left" |2>-[[parcstats|parcstats3]] ||<style="text-align:left" |2>label/?h.aparc.a2009s.annot ||<style="text-align:left" |2>[[mris_anatomical_stats]] -mgz -f stats/?h.aparc.DKTatlas.stats -b -a label/?h.aparc.DKTatlas.annot -c label/aparc.annot.DKTatlas.ctab <subjid> ?h ||stats/?h.aparc.a2009s.stats ||
||stats/aparc.annot.a2009s.ctab ||
||<style="text-align:left;" |4>-pctsurfcon ||rawavg.mgz ||<style="text-align:left;" |4>pctsurfcon --s <subjid> --?h-only ||<style="text-align:left;" |2>?h.w-g.pct.mgh ||
||orig.mgz ||
||?h.cortex.label ||<style="text-align:left" |2>stats/?h.w-g.pct.stats ||
||?h.white ||
||<style="text-align:left;" |3>-[[cortribbon]] ||aseg.presurf.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;" |2>?h.ribbon.mgz ||
||?h.white ||
||?h.pial ||<style="text-align:left" |1>ribbon.mgz ||
||<style="text-align:left" |2>-hyporelabel ||<style="text-align:left" |1>aseg.presurf.mgz ||<style="text-align:left" |2>mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz ||<style="text-align:left" |2>aseg.presurf.hypos.mgz ||
||?h.white ||
||<style="text-align:left;" |8>-[[aparc2aseg]] ||aseg.presurf.hypos.mgz ||<style="text-align:left;" |4>[[mri_aparc2aseg]] --s <subjid> --ribbon ||<style="text-align:left;" |4>aparc+aseg.mgz ||
||?h.ribbon.mgz ||
||label/?h.aparc.annot ||
||<style="text-align:left">ribbon.mgz ||
||aseg.presurf.hypos.mgz ||<style="text-align:left;" |4>[[mri_aparc2aseg]] --s <subjid> --ribbon --a2009s ||<style="text-align:left;" |4>aparc.a2009s+aseg.mgz ||
||?h.ribbon.mgz ||
||label/?h.aparc.a2009s.annot ||
||<style="text-align:left">ribbon.mgz ||
||<style="text-align:left;" |1>-apas2aseg ||aparc+aseg.mgz ||<style="text-align:left;" |1>apas2aseg --i aparc+aseg.mgz --o aseg.mgz ||<style="text-align:left;" |1>aseg.mgz ||
||<style="text-align:left" |2>-[[segstats]] ||aseg.mgz ||<style="text-align:left" |2>[[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 --totalgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab $FREESURFER_HOME/ASegStatsLUT.txt --subject <subjid> ||<style="text-align:left" |2>stats/aseg.stats ||
||norm.mgz ||
||<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 --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 ||