Diff for "ReconAllDevTable" - Free Surfer Wiki

Differences between revisions 3 and 264 (spanning 261 versions)

FreeSurfer Tutorial: Process Flow

This table shows the recon-all steps for the current dev version of FreeSurfer (available here). It does not document the stable, publicly released, version of Freesurfer.

Updated April 2015 NJS

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
			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 -c ctrl_pts.mgz -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 -relabel_unlikely 9 .3 -prior 0.5 -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 -lta <subjid>/mri/transforms/cc_up.lta -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 -aseg ../mri/aseg.presurf -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 ?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 -orig_white white -orig_pial white -fix_mtl -aseg ../mri/aseg.presurf -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	orig/T2raw.mgz	bbregister --s <subjid> --mov mri/orig/T2raw.mgz --lta mri/transforms/T2raw.lta --init-fsl --T2	transforms/T2raw.lta
		orig/T2raw.mgz	mri_convert -odt short -at mri/transforms/T2raw.lta -rt cubic -ns 1 -rl mri/orig.mgz mri/orig/T2raw.mgz mri/T2.prenorm.mgz	T2.prenorm.mgz
		transforms/T2raw.lta
		aseg.presurf.mgz	mri_normalize -sigma 0.5 -nonmax_suppress 0 -min_dist 1 -aseg mri/aseg.presurf.mgz -surface surf/rh.white identity.nofile -surface surf/lh.white identity.nofile mri/T2.prenorm.mgz mri/T2.mgz	T2.mgz
		?h.white
		T2.prenorm.mgz
		?h.pial	cp -v surf/?h.pial surf/?h.woT2.pial	?h.woT2.pial
		aseg.presurf.mgz	mris_make_surfaces -orig_white white -orig_pial woT2.pial -aseg ../mri/aseg.presurf -nowhite -mgz -T1 brain.finalsurfs -T2 ../mri/T2 -nsigma_above 2 -nsigma_below 5 <subjid> ?h	?h.pial
		brain.finalsurfs.mgz
		wm.mgz
		filled.mgz		?h.curv.pial
		?h.white
		label/?h.aparc.annot		?h.area.pial
		T2.mgz		?h.thickness
		?h.woT2.pial
	-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
	-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
	-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
		wm.mgz, ribbon.mgz		label/aparc.annot.ctab
		?h.white
		?h.pial
		?h.thickness
	-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
		wm.mgz, ribbon.mgz		label/aparc.annot.a2009s.ctab
		?h.white
		?h.pial
		?h.thickness
	-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.DKTatlas40.annot
		?h.sphere.reg
		label/?h.cortex.label
	-parcstats3	label/?h.aparc.DKTatlas40.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.DKTatlas40.stats
		wm.mgz, ribbon.mgz		label/aparc.annot.DKTatlas40.ctab
		?h.white
		?h.pial
		?h.thickness
	-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
-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	brainmask.mgz, norm.mgz, aseg.mgz, aseg.presurf.mgz, ribbon.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
	?h.orig.nofix, ?h.white, ?h.pial
-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
	talairach.xfm, brainmask.mgz, norm.mgz, ribbon.mgz, wmparc.mgz, aseg.presurf.mgz, ?h.white, ?h.pial	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 3 as of 2006-01-09 18:33:32 → 
  Size: 7571
  Editor: JenniPacheco
  Comment:
+   ← Revision 264 as of 2015-05-08 14:10:48 → ⇥
  Size: 20185
  Editor: NickSchmansky
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
+#acl LcnGroup:read,write,delete,revert All:read
-Line 2:
+Line 3:
+This table shows the recon-all steps for the current '''dev''' version of FreeSurfer [[ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/|(available here)]].  It does not document the stable, publicly released, version of Freesurfer.

''Updated April 2015 NJS''

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

See also the OtherUsefulFlags for other recon-all options.
||<tablestyle="text-align:left;       ;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 || ||
|| ||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 31:
-||<rowbgcolor='#80FF80'>'''recon-all-dev 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||
||<|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||
||<rowbgcolor='#E0E0FF'>orig/002.mgz||
||<rowbgcolor='#E0E0FF'>rawavg.mgz||["mri_convert"] rawavg.mgz orig.mgz --conform||orig.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||
||<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||
||<|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||
||<-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||
+||<tablestyle="text-align:left;       ;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]] -c ctrl_pts.mgz -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]] -relabel_unlikely 9 .3 -prior 0.5 -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]] -lta <subjid>/mri/transforms/cc_up.lta -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]] -aseg ../mri/aseg.presurf -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 ?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 63:
+Line 106:
-Click here to see a table of OtherUsefulFlags
+||<tablestyle="text-align:left;       ;text-align:left">'''recon-all step''' ||'''Individual Flag''' ||'''Input''' ||'''Command Line''' ||'''Output''' ||
||<style="text-align:left;" |83>'''[[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]] -orig_white white -orig_pial white -fix_mtl -aseg ../mri/aseg.presurf -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;" |15>-T2pial ''or'' <<BR>>-FLAIRpial ''optional'' ||orig/T2raw.mgz ||bbregister --s <subjid> --mov mri/orig/T2raw.mgz --lta mri/transforms/T2raw.lta --init-fsl --T2 ||transforms/T2raw.lta ||
||orig/T2raw.mgz ||<style="text-align:left" |2>mri_convert -odt short -at mri/transforms/T2raw.lta -rt cubic -ns 1 -rl mri/orig.mgz mri/orig/T2raw.mgz mri/T2.prenorm.mgz ||<style="text-align:left" |2>T2.prenorm.mgz ||
||transforms/T2raw.lta ||
||aseg.presurf.mgz ||<style="text-align:left" |3>mri_normalize -sigma 0.5 -nonmax_suppress 0 -min_dist 1 -aseg mri/aseg.presurf.mgz -surface surf/rh.white identity.nofile -surface surf/lh.white identity.nofile mri/T2.prenorm.mgz mri/T2.mgz ||<style="text-align:left" |3>T2.mgz ||
||?h.white ||
||T2.prenorm.mgz ||
||?h.pial ||cp -v surf/?h.pial surf/?h.woT2.pial ||?h.woT2.pial ||
||aseg.presurf.mgz ||<style="text-align:left" |8>[[mris_make_surfaces]] -orig_white white -orig_pial woT2.pial -aseg ../mri/aseg.presurf -nowhite -mgz -T1 brain.finalsurfs -T2 ../mri/T2 -nsigma_above 2 -nsigma_below 5 <subjid> ?h ||<style="text-align:left" |3>?h.pial ||
||brain.finalsurfs.mgz ||
||wm.mgz ||
||filled.mgz ||<style="text-align:left" |2>?h.curv.pial ||
||?h.white ||
||<style="text-align:left" |1>label/?h.aparc.annot ||<style="text-align:left" |1>?h.area.pial ||
||<style="text-align:left" |1>T2.mgz ||<style="text-align:left" |2>?h.thickness ||
||?h.woT2.pial ||
||<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;" |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" |5>-[[parcstats]] ||<style="text-align:left" |1>label/?h.aparc.annot ||<style="text-align:left" |5>[[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 ||
||<style="text-align:left" |1>wm.mgz, ribbon.mgz ||<style="text-align:left" |4>label/aparc.annot.ctab ||
||?h.white ||
||?h.pial ||
||?h.thickness ||
||<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" |5>-[[parcstats|parcstats2]] ||<style="text-align:left" |1>label/?h.aparc.a2009s.annot ||<style="text-align:left" |5>[[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 ||
||<style="text-align:left" |1>wm.mgz, ribbon.mgz ||<style="text-align:left" |4>label/aparc.annot.a2009s.ctab ||
||?h.white ||
||?h.pial ||
||?h.thickness ||
||<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.DKTatlas40.annot ||
||?h.sphere.reg ||
||label/?h.cortex.label ||
||<style="text-align:left" |5>-[[parcstats|parcstats3]] ||<style="text-align:left" |1>label/?h.aparc.DKTatlas40.annot ||<style="text-align:left" |5>[[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.DKTatlas40.stats ||
||<style="text-align:left" |1>wm.mgz, ribbon.mgz ||<style="text-align:left" |4>label/aparc.annot.DKTatlas40.ctab ||
||?h.white ||
||?h.pial ||
||?h.thickness ||
||<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" |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]] ||brainmask.mgz, norm.mgz, aseg.mgz, aseg.presurf.mgz, ribbon.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 ||
||?h.orig.nofix, ?h.white, ?h.pial ||
||<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 ||
||talairach.xfm, brainmask.mgz, norm.mgz, ribbon.mgz, wmparc.mgz, aseg.presurf.mgz, ?h.white, ?h.pial ||<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 ||