Diff for "OtherUsefulFlags" - Free Surfer Wiki

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FreeSurfer Tutorial: Useful recon-all flags.

This page extends ReconAllDevTable. The following flags can be used in conjunction with individual steps or the entire process:

-autorecon-all	either of these flags will work to run the entire recon-all process.
-all
-clean-tal	trashes any manual edits to the talairach, makes talairach.xfm and talairach.auto.xfm the same and runs using the automatically generated talairach.xfm
-clean-seed	trashes all saved seed point for the cutting planes and uses the automatically set cutting planes.
-clean-cp	trashes control points and runs the normalization without control points.
-clean-bm	trashes any manual edits to the brainmask.mgz volume, makes brainmask.mgz and brainmask.auto.mgz the same and runs using the automatically generated brainmask.mgz
-clean-wm	trashes any manual edits to the wm.mgz volume and runs using the automatically generated wm.mgz.
-clean-aseg	trashes any manual edits to the aseg.mgz and runs using the automatically generated aseg.mgz
-clean-cpwm	combination of -clean-cp and -clean-wm.
-clean-xopts	delete pre-existing expert options file
-clean-cw256
-clean-lta	moves *.lta files to trash
-clean-pfh	trashes preflood height volumes (skullstrip)
-clean-bfse	trashes edits to brain.finalsurfs.manedit.mgz
-clean	use this flag to clear all of your manual edits and run it completely fresh.
-deface	removes the face from the orig volume to anonymize it.
-dontrun	useful for debugging. just prints the commands that will run (does not execute them).
-gcut	use this flag when skull strip leaves a little bit of dura behind. In this case, adjusting the watershed parameters won't be as useful and manual edits will take too long. INFO: Care must be taken to thoroughly inspect your data when using -gcut. In particular, inpsect the edges of gm and cerebellum for over-aggressive cutting. Add -segmentation brainmask.gcuts.mgz to tkmedit to view the voxels which gcut has removed.
-mprage	changes some of the assumptions about CNR and SNR, and will use a higher threshold to allow the control points to grow more liberally than in general.
-3T	Enables the two 3T specific options that recon-all supports: nu intensity correction params, and the special schwartz atlas
-multistrip	use this flag on a subject when you would like to get skullstrip results using several different watershed preflood heights simultaneously. Output will be nu, orig, and T1 volumes stripped at these heights: 5, 10, 20, 30. You can change which preflood heights are used by setting this variable first: setenv WATERSHED_PREFLOOD_HEIGHTS '20 30 40 50'. Be sure to use -clean-bm with this flag.
-noaseg	use this flag on subjects that either cannot use an aseg (i.e., baby brains or non-human primates) or for those for which you will never want an aseg. It skips the subcortical segmentation and will not try and use it (aseg.mgz) in any of the subsequent steps.
-norandomness	use this flag on a subject when it is necessary to ensure that results are exactly the same from run to run. it seeds the random number generator used by some algorithms with the same number, removing any variability.
-notal-check	use this flag when running a subject after receiving an error about Tailarach Failure Detection and the tailarach transform looks fine after checking it with this command line: tkregister2 --mgz --s <subjid> --fstal
-no-wsgcaatlas	use this flag when you have reason to believe that certain anatomy could be an outlier, and is responsible for causing the skullstripping step to fail or produce poor skullstripping (wsgcaatlas = with skull gaussian classifier array atlas)
-surfsegedit	this flag fixes the gm and a few other areas in the aseg using info from the surfaces. Run after the surfaces are done.
-time	this flag can be added to report the time each step takes
-canorm-usecps	This flag uses control points to change the aseg. This can be particularly useful when you have an overlabeled putamen (the strategy would be to put the control points in white matter surrounding the putamen. It is advised to do these types of edits first before using control points to edit the surfaces (the default use of control points).
-vno_match_check	Confirms that the surface data is out of sync in case an error indicates that there is a size mismatch. Then run from whatever stage that is out of sync.

recon-all flag	Used with step	Description
-no-ca-align	-careg	this flag should be used if the data to be processed comes from the same scanner platform and pulse sequence as the atlas. With the FreeSurfer RB40 atlas this means MPRAGE on a 1.5T Siemens scanner.
-no-ca-align	-calabel
-subcortseg	-gcareg	runs the subcortical segmentation and associated statistics
	-canorm
	-careg
	-rmneck
	-skull-lta
	-calabel
	-segstats
-cc-crs <c r s>	-fill	manually sets the corpus callosum seed point
-pons-crs <c r s>	-fill	manually sets the pons seed point
-rh-crs <c r s>	-fill	manually sets the right hemisphere seed point
-lh-crs <c r s>	-fill	manually sets the left hemisphere seed point
-jacobian_dist0		Computes how much an individual surface must be distorted in order to perfectly match the atlas (ie, distance contraints are turned off).

The following flags can be used after certain manual intervention to regenerate accurate volumes and surfaces (if a data set has or needs spherical morphing, add the -autorecon3 flag):

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
	-nuintensitycor	orig.mgz	mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2	nu.mgz
	-nuintensitycor	talairach.xfm		nu.mgz
	-normalization	nu.mgz	mri_normalize -g 1 -mprage nu.mgz T1.mgz	T1.mgz
	-skullstrip	nu.mgz	mri_em_register -skull nu.mgz $FREESURFER_HOME/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta	transforms/talairach_with_skull.lta
		T1.mgz	mri_watershed -T1 -brain_atlas $FREESURFER_HOME/average/RB_all_withskull_2016-05-10.vc700.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>
	-gcareg	brainmask.mgz	mri_em_register -uns 3 -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB_all_2016-05-10.vc700.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_2016-05-10.vc700.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_2016-05-10.vc700.gca transforms/talairach.m3z	transforms/talairach.m3z
		transforms/talairach.lta
		norm.mgz
	-calabel	norm.mgz	mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2016-05-10.vc700.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 -mprage -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 -mprage 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 -aseg ../mri/aseg.presurf -nowhite -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
	-cortribbon	aseg.presurf.mgz	mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon <subjid>	?h.ribbon.mgz
		?h.white
		?h.pial		ribbon.mgz
	-parcstats	label/?h.aparc.annot	mris_anatomical_stats -th3 -mgz -cortex ../label/?h.cortex.label -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 -th3 -mgz -cortex ../label/?h.cortex.label -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.DKTatlas.2016-03-20.gcs ../label/?h.aparc.DKTatlas.annot	label/?h.aparc.DKTatlas.annot
		?h.sphere.reg
		label/?h.cortex.label
	-parcstats3	label/?h.aparc.DKTatlas.annot	mris_anatomical_stats -th3 -mgz -cortex ../label/?h.cortex.label -f stats/?h.aparc.DKTatlas.stats -b -a label/?h.aparc.DKTatlas.annot -c label/aparc.annot.DKTatlas.ctab <subjid> ?h	stats/?h.aparc.DKTatlas.stats
		wm.mgz, ribbon.mgz		label/aparc.annot.DKTatlas.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 --annot aparc.a2009s	aparc.a2009s+aseg.mgz
?h.ribbon.mgz
label/?h.aparc.a2009s.annot
ribbon.mgz
aseg.presurf.hypos.mgz		mri_aparc2aseg --s <subjid> --ribbon --annot aparc.DKTatlas	aparc.DKTatlas+aseg.mgz
?h.ribbon.mgz
label/?h.aparc.DKTatlas.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*_exvivo.label label/?h.perirhinal_exvivo.label label/?h.entorhinal_exvivo.label

-Deletions are marked like this.
+Additions are marked like this.
 Line 49:
-||<bgcolor='#FFFFE0'>'''-cc-xyz <X Y Z>'''||<bgcolor='#FFFFE0'>-fill||<bgcolor='#E0E0FF'>manually sets the corpus callosum seed point||

||<bgcolor='#FFFFE0'>'''-pons-xyz <X Y Z>'''||<bgcolor='#FFFFE0'>-fill||<bgcolor='#E0E0FF'>manually sets the pons seed point||

||<bgcolor='#FFFFE0'>'''-rh-xyz <X Y Z>'''||<bgcolor='#FFFFE0'>-fill||<bgcolor='#E0E0FF'>manually sets the right hemisphere seed point||

||<bgcolor='#FFFFE0'>'''-lh-xyz <X Y Z>'''||<bgcolor='#FFFFE0'>-fill||<bgcolor='#E0E0FF'>manually sets the left hemisphere seed point||
+||<bgcolor='#FFFFE0'>'''-cc-crs <c r s>'''||<bgcolor='#FFFFE0'>-fill||<bgcolor='#E0E0FF'>manually sets the corpus callosum seed point||

||<bgcolor='#FFFFE0'>'''-pons-crs <c r s>'''||<bgcolor='#FFFFE0'>-fill||<bgcolor='#E0E0FF'>manually sets the pons seed point||

||<bgcolor='#FFFFE0'>'''-rh-crs <c r s>'''||<bgcolor='#FFFFE0'>-fill||<bgcolor='#E0E0FF'>manually sets the right hemisphere seed point||

||<bgcolor='#FFFFE0'>'''-lh-crs <c r s>'''||<bgcolor='#FFFFE0'>-fill||<bgcolor='#E0E0FF'>manually sets the left hemisphere seed point||
 Line 54:
-||<|9(bgcolor='#FFFFE0'>'''-old-atlas'''||

||<bgcolor='#FFFFE0'>-gcareg||<|8(bgcolor='#E0E0FF'>Use this flag in conjunction with other steps of recon-all and it will default to the old set of atlases.  Uses talairach_mixed.gca for the subcortical segmentation, ?h.average.tif for the surface morph, and ?h.atlas2002_simple.gcs for the cortical parcellations.||

||<bgcolor='#FFFFE0'>-canorm||

||<bgcolor='#FFFFE0'>-careg||

||<bgcolor='#FFFFE0'>-calabel||

||<bgcolor='#FFFFE0'>-surfreg||

||<bgcolor='#FFFFE0'>-contrasurfreg||

||<bgcolor='#FFFFE0'>-avgcurv||

||<bgcolor='#FFFFE0'>-cortparc||
-Line 67:
+Line 58:
-||<rowbgcolor='#80FF80'>'''recon-all step'''||'''Individual Flag'''||'''Input'''||'''Command Line'''||'''Output'''||

||<|31(bgcolor='#FFFFE0'>'''[[recon-all]] -autorecon2-wm -subjid subj '''(use this after doing manual wm edits.  This flag will regenerate all necessary volumes and surfaces)||

||<|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 ||
+||<tablestyle="text-align:left;        ;text-align:left">'''recon-all step''' ||'''Individual Flag''' ||'''Input''' ||'''Command Line''' ||'''Output''' ||

||<style="text-align:left" |20>'''[[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 ||

||<style="text-align:left;" |2>-[[nuintensitycor]] ||orig.mgz ||<style="text-align:left;" |2>[[mri_nu_correct.mni]] --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 ||<style="text-align:left;" |2>nu.mgz ||

||talairach.xfm ||

||<style="text-align:left" |1>-[[normalization]] ||nu.mgz ||[[mri_normalize]] -g 1 -mprage nu.mgz T1.mgz ||T1.mgz ||

||<style="text-align:left" |3>-[[skullstrip]] ||nu.mgz ||[[mri_em_register]] -skull nu.mgz $FREESURFER_HOME/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta ||transforms/talairach_with_skull.lta ||

||T1.mgz ||[[mri_watershed]] -T1 -brain_atlas $FREESURFER_HOME/average/RB_all_withskull_2016-05-10.vc700.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 ||





||<tablestyle="text-align:left;        ;text-align:left">'''recon-all step''' ||'''Individual Flag''' ||'''Input''' ||'''Command Line''' ||'''Output''' ||

||<style="text-align:left;" |69>'''[[recon-all]] -autorecon2 -subjid <subjid>''' ||

||<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_2016-05-10.vc700.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_2016-05-10.vc700.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_2016-05-10.vc700.gca transforms/talairach.m3z ||<style="text-align:left;" |3>transforms/talairach.m3z ||

||transforms/talairach.lta ||

||norm.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 norm.mgz transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2016-05-10.vc700.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]] -mprage -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]] -mprage 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 ||
-Line 75:
+Line 111:
-||filled.mgz ||<|2(bgcolor='#E0E0FF'>[[mri_pretess]] filled.mgz 127 norm.mgz filled-pretess127.mgz ||<|2(bgcolor='#E0E0FF'> filled-pretess127.mgz ||
+||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 ||
-Line 78:
+Line 114:
-||?h.orig.nofix ||[[mris_extract_main_component]] ?h.orig.nofix ?h.orig.nofix ||?h.orig.nofix ||
+||?h.orig.nofix ||mris_extract_main_component ?h.orig.nofix ?h.orig.nofix ||?h.orig.nofix ||
-Line 80:
+Line 116:
-||<bgcolor='#FFFFE0'>-smooth1||<bgcolor='#E0E0FF'>?h.orig.nofix||<bgcolor='#E0E0FF'>[[mris_smooth]] -nw ?h.orig.nofix ?h.smoothwm.nofix||<bgcolor='#E0E0FF'>?h.smoothwm.nofix||

||<bgcolor='#FFFFE0'>-inflate1||<bgcolor='#E0E0FF'>?h.smoothwm.nofix||<bgcolor='#E0E0FF'>[[mris_inflate]] -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 -0 ?h.inflated.nofix ?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 || ||

||<|5(bgcolor='#FFFFE0'>-white ||<|1(bgcolor='#E0E0FF'>aseg.mgz, brain.finalsurfs.mgz, wm.mgz, filled.mgz ||<|5(bgcolor='#E0E0FF'>[[mris_make_surfaces]] -whiteonly -noaparc -mgz -T1 brain.finalsurfs <subjid> ?h ||?h.white ||

||<|4(bgcolor='#E0E0FF'>?h.orig ||
+||-[[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 ||
-Line 92:
+Line 131:
-||?h.area||
+||?h.area ||
-Line 94:
+Line 133:
-||<bgcolor='#FFFFE0'>-smooth2 ||?h.white ||<bgcolor='#E0E0FF'>[[mris_smooth]] -n 3 -nw ?h.white ?h.smoothwm ||?h.smoothwm ||

||<|4(bgcolor='#FFFFE0'>-inflate2 ||<|2(bgcolor='#E0E0FF'>?h.smoothwm ||<|2(bgcolor='#E0E0FF'>[[mris_inflate]] ?h.smoothwm ?h.inflated ||?h.inflated ||

||<bgcolor='#E0E0FF'>?h.sulc ||

||<|2(bgcolor='#E0E0FF'>?h.inflated ||<|2(bgcolor='#E0E0FF'>[[mris_curvature]] -thresh .999 -n -a 5 -w -distances 10 10 ?h.inflated ||?h.inflated.H ||
+||-[[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 ||
-Line 99:
+Line 140:
-||<rowbgcolor='#80FF80'>'''recon-all step'''||'''Individual Flag'''||'''Input'''||'''Command Line'''||'''Output'''||

||<|42(bgcolor='#FFFFE0'>'''[[recon-all]] -autorecon2-noaseg -subjid subj '''(use this after doing manual edits to the aseg.  This flag will regenerate all final surfaces)||

||<|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 ||brain.mgz ||<|2(bgcolor='#E0E0FF'>[[mri_mask]] -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz ||<|2(bgcolor='#E0E0FF'>brain.finalsurfs.mgz ||

||brainmask.mgz ||

||<|6(bgcolor='#FFFFE0'>-segmentation ||brain.mgz ||[[mri_segment]] brain.mgz wm.seg.mgz ||wm.seg.mgz ||

||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 ||

||aseg.mgz ||

||brain.mgz ||

||wm.asegedit.mgz ||<|2(bgcolor='#E0E0FF'>[[mri_pretess]] wm.asegedit.mgz wm norm.mgz wm.mgz ||<|2(bgcolor='#E0E0FF'>wm.mgz ||

||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 ||

||norm.mgz ||

||filled-pretess255.mgz ||[[mri_tessellate]] filled-pretess255.mgz 255 lh.orig.nofix ||lh.orig.nofix ||

||filled.mgz ||<|2(bgcolor='#E0E0FF'>[[mri_pretess]] filled.mgz 127 norm.mgz filled-pretess127.mgz ||<|2(bgcolor='#E0E0FF'> 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 || ||

||<bgcolor='#FFFFE0'>-smooth1||<bgcolor='#E0E0FF'>?h.orig.nofix||<bgcolor='#E0E0FF'>[[mris_smooth]] -nw ?h.orig.nofix ?h.smoothwm.nofix||<bgcolor='#E0E0FF'>?h.smoothwm.nofix||

||<bgcolor='#FFFFE0'>-inflate1||<bgcolor='#E0E0FF'>?h.smoothwm.nofix||<bgcolor='#E0E0FF'>[[mris_inflate]] -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 -0 ?h.inflated.nofix ?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 || ||

||<|5(bgcolor='#FFFFE0'>-white ||<|1(bgcolor='#E0E0FF'>aseg.mgz, brain.finalsurfs.mgz, wm.mgz, filled.mgz ||<|5(bgcolor='#E0E0FF'>[[mris_make_surfaces]] -whiteonly -noaparc -mgz -T1 brain.finalsurfs <subjid> ?h ||?h.white ||

||<|4(bgcolor='#E0E0FF'>?h.orig ||

||?h.curv ||

||?h.area||

||?h.cortex.label ||

||<bgcolor='#FFFFE0'>-smooth2 ||?h.white ||<bgcolor='#E0E0FF'>[[mris_smooth]] -n 3 -nw ?h.white ?h.smoothwm ||?h.smoothwm ||

||<|4(bgcolor='#FFFFE0'>-inflate2 ||<|2(bgcolor='#E0E0FF'>?h.smoothwm ||<|2(bgcolor='#E0E0FF'>[[mris_inflate]] ?h.smoothwm ?h.inflated ||?h.inflated ||

||<bgcolor='#E0E0FF'>?h.sulc ||

||<|2(bgcolor='#E0E0FF'>?h.inflated ||<|2(bgcolor='#E0E0FF'>[[mris_curvature]] -thresh .999 -n -a 5 -w -distances 10 10 ?h.inflated ||?h.inflated.H ||

||?h.inflated.K ||



||<rowbgcolor='#80FF80'>'''recon-all step'''||'''Individual Flag'''||'''Input'''||'''Command Line'''||'''Output'''||

||<|47(bgcolor='#FFFFE0'>'''[[recon-all]] -autorecon-pial -subjid subj '''(use this after editing brainmask.mgz or brain.finalsurfs.mgz to alter pial surface.  This flag will regenerate all final surfaces) <<BR>><<BR>>**note** this flag includes all the steps in -autorecon3 therefore it is not necessary to pass the -autorecon3 flag after this||

||<|2(bgcolor='#FFFFE0'>-maskbfs ||brain.mgz ||<|2(bgcolor='#E0E0FF'>[[mri_mask]] -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz ||<|2(bgcolor='#E0E0FF'>brain.finalsurfs.mgz ||

||brainmask.mgz ||

||<|5(bgcolor='#FFFFE0'>-white ||<|1(bgcolor='#E0E0FF'>aseg.mgz, brain.finalsurfs.mgz, wm.mgz, filled.mgz ||<|5(bgcolor='#E0E0FF'>[[mris_make_surfaces]] -whiteonly -noaparc -mgz -T1 brain.finalsurfs <subjid> ?h ||?h.white ||

||<|4(bgcolor='#E0E0FF'>?h.orig ||

||?h.curv ||

||?h.area||

||?h.cortex.label ||

||<bgcolor='#FFFFE0'>-smooth2 ||?h.white ||<bgcolor='#E0E0FF'>[[mris_smooth]] -n 3 -nw ?h.white ?h.smoothwm ||?h.smoothwm ||

||<|4(bgcolor='#FFFFE0'>-inflate2 ||<|2(bgcolor='#E0E0FF'>?h.smoothwm ||<|2(bgcolor='#E0E0FF'>[[mris_inflate]] ?h.smoothwm ?h.inflated ||?h.inflated ||

||<bgcolor='#E0E0FF'>?h.sulc ||

||<|2(bgcolor='#E0E0FF'>?h.inflated ||<|2(bgcolor='#E0E0FF'>[[mris_curvature]] -thresh .999 -n -a 5 -w -distances 10 10 ?h.inflated ||?h.inflated.H ||

||?h.inflated.K ||

||<bgcolor='#FFFFE0'>-sphere ||?h.inflated,?h.smoothwm ||[[mris_sphere]] ?h.inflated ?h.sphere ||?h.sphere ||

||<bgcolor='#FFFFE0'>-surfreg ||?h.sphere ||[[mris_register]] -curv ?h.sphere $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif ?h.sphere.reg ||?h.sphere.reg ||

||<|2(bgcolor='#FFFFE0'>-jacobian_white ||?h.white ||<|2(bgcolor='#E0E0FF'>[[mris_jacobian]] ?h.white ?h.sphere.reg ?h.jacobian_white ||<|2(bgcolor='#E0E0FF'>?h.jacobian_white ||

||?h.sphere.reg ||

||<bgcolor='#FFFFE0'>-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 ||

||<|2(bgcolor='#FFFFE0'>-cortparc ||aseg.mgz, ?h.cortex.label ||<|2(bgcolor='#E0E0FF'>[[mris_ca_label]] -l ../label/lh.cortex.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 ||

||?h.sphere.reg ||

||<|4(bgcolor='#FFFFE0'>-pial ||<|1(bgcolor='#E0E0FF'>aseg.mgz, brain.finalsurfs.mgz, wm.mgz, filled.mgz ||<|4(bgcolor='#E0E0FF'>[[mris_make_surfaces]] -white NOWRITE -mgz -T1 brain.finalsurfs <subjid> ?h ||?h.pial ||

||<|3(bgcolor='#E0E0FF'>?h.orig, label/?h.aparc.annot ||

||?h.curv.pial, ?h.area.pial||

||?h.thickness||

||<|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 ||

||?h.area.pial ||

||<|1(bgcolor='#E0E0FF'>?h.area.mid ||<|1(bgcolor='#E0E0FF'>[[mris_calc]] -o ?h.area.mid ?h.area.mid div 2 ||?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 ||
+||<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 ||





||<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 -aseg ../mri/aseg.presurf -nowhite -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;" |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 <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]] -th3 -mgz -cortex ../label/?h.cortex.label -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 ||
-Line 175:
+Line 187:
-||<bgcolor='#FFFFE0'>-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 ||

||<|2(bgcolor='#FFFFE0'>-cortparc2 ||aseg.mgz, ?h.cortex.label ||<|2(bgcolor='#E0E0FF'>[[mris_ca_label]] -l ../label/lh.cortex.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 ||

||?h.sphere.reg ||

||<bgcolor='#FFFFE0'>-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 ||

||<|3(bgcolor='#FFFFE0'>-cortribbon ||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, ribbon.mgz  ||
+||<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]] -th3 -mgz -cortex ../label/?h.cortex.label -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 ||
-Line 182:
+Line 194:
-||<bgcolor='#FFFFE0'>-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 ||

||<|6(bgcolor='#FFFFE0'>-aparc2aseg ||aseg.mgz ||<style="text-align: left;" |3>[[mri_aparc2aseg]] --s <subjid> --ribbon ||<|3(bgcolor='#E0E0FF'>aparc+aseg.mgz ||

||?h.ribbon.mgz||
+||?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.DKTatlas.2016-03-20.gcs ../label/?h.aparc.DKTatlas.annot ||<style="text-align:left;" |3>label/?h.aparc.DKTatlas.annot ||

||?h.sphere.reg ||

||label/?h.cortex.label ||

||<style="text-align:left" |5>-[[parcstats|parcstats3]] ||<style="text-align:left" |1>label/?h.aparc.DKTatlas.annot ||<style="text-align:left" |5>[[mris_anatomical_stats]] -th3 -mgz -cortex ../label/?h.cortex.label -f stats/?h.aparc.DKTatlas.stats -b -a label/?h.aparc.DKTatlas.annot -c label/aparc.annot.DKTatlas.ctab <subjid> ?h ||stats/?h.aparc.DKTatlas.stats ||

||<style="text-align:left" |1>wm.mgz, ribbon.mgz ||<style="text-align:left" |4>label/aparc.annot.DKTatlas.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;" |12>-[[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 ||
-Line 186:
+Line 212:
-||aseg.mgz ||<|3(bgcolor='#E0E0FF'>[[mri_aparc2aseg]] --s <subjid> --ribbon --a2009s ||<|3(bgcolor='#E0E0FF'>aparc.a2009s+aseg.mgz ||
+||<style="text-align:left">ribbon.mgz ||

||aseg.presurf.hypos.mgz ||<style="text-align:left;" |4>[[mri_aparc2aseg]] --s <subjid> --ribbon --annot aparc.a2009s ||<style="text-align:left;" |4>aparc.a2009s+aseg.mgz ||
-Line 189:
+Line 216:
-||<|2(bgcolor='#FFFFE0'>-wmparc ||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 ||

||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 ||

||<bgcolor='#FFFFE0'>-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||

||<bgcolor='#FFFFE0'>-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||





||<rowbgcolor='#80FF80'>'''recon-all step'''||'''Individual Flag'''||'''Input'''||'''Command Line'''||'''Output'''||

||<|17(bgcolor='#FFFFE0'>'''[[recon-all]] -autorecon2-perhemi -subjid subj '''(use this to run only the steps that are run per-hemisphere, in conjunction with the '-hemi' flag.  This is useful if one hemisphere failed and you need to run them separately)||

||<|2((bgcolor='#FFFFE0'>-tessellate||<|2(bgcolor='#E0E0FF'>filled.mgz||<bgcolor='#E0E0FF'>[[mri_tessellate]] filled.mgz 255 ../surf/lh.orig.nofix||<bgcolor='#E0E0FF'>lh.orig.nofix||

||<rowbgcolor='#E0E0FF'>[[mri_tessellate]] filled.mgz 127 ../surf/rh.orig.nofix||rh.orig.nofix||

||<bgcolor='#FFFFE0'>-smooth1||<bgcolor='#E0E0FF'>?h.orig.nofix||<bgcolor='#E0E0FF'>[[mris_smooth]] -nw ?h.orig.nofix ?h.smoothwm.nofix||<bgcolor='#E0E0FF'>?h.smoothwm.nofix||

||<bgcolor='#FFFFE0'>-inflate1||<bgcolor='#E0E0FF'>?h.smoothwm.nofix||<bgcolor='#E0E0FF'>[[mris_inflate]] -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 -0 ?h.inflated.nofix ?h.inflated.nofix ?h.qsphere.nofix||<bgcolor='#E0E0FF'>?h.qsphere.nofix||

||<|3(bgcolor='#FFFFE0'>-fix||<bgcolor='#E0E0FF'>?h.orig.nofix||<bgcolor='#E0E0FF'>cp ?h.orig.nofix ?h.orig||<bgcolor='#E0E0FF'>?h.orig||

||<bgcolor='#E0E0FF'>?h.inflated.nofix||<bgcolor='#E0E0FF'>cp ?h.inflated.nofix ?h.inflated||<bgcolor='#E0E0FF'>?h.inflated||

||<bgcolor='#E0E0FF'>?h.qsphere.nofix||<bgcolor='#E0E0FF'>[[mris_fix_topology]] -errors -mgz -sphere qsphere.nofix -ga <subjid> ?h||<bgcolor='#E0E0FF'>?h.orig||

||<bgcolor='#FFFFE0'>-smooth2||<bgcolor='#E0E0FF'>?h.white||<bgcolor='#E0E0FF'>[[mris_smooth]] ?h.white ?h.smoothwm||<bgcolor='#E0E0FF'>?h.smoothwm||

||<|2(bgcolor='#FFFFE0'>-inflate2||<|2(bgcolor='#E0E0FF'>?h.white||<|2(bgcolor='#E0E0FF'>[[mris_inflate]] ?h.white ?h.inflated||<bgcolor='#E0E0FF'>?h.inflated||

||<(rowbgcolor='#E0E0FF'>?h.sulc||

||<|5(bgcolor='#FFFFE0'>-white ||<|1(bgcolor='#E0E0FF'>aseg.mgz, brain.finalsurfs.mgz, wm.mgz, filled.mgz ||<|5(bgcolor='#E0E0FF'>[[mris_make_surfaces]] -whiteonly -noaparc -mgz -T1 brain.finalsurfs <subjid> ?h ||?h.white ||

||<|4(bgcolor='#E0E0FF'>?h.orig ||

||?h.curv ||

||?h.area||

||?h.cortex.label ||
+||<style="text-align:left">ribbon.mgz ||

||aseg.presurf.hypos.mgz ||<style="text-align:left;" |4>[[mri_aparc2aseg]] --s <subjid> --ribbon --annot aparc.DKTatlas ||<style="text-align:left;" |4>aparc.DKTatlas+aseg.mgz ||

||?h.ribbon.mgz ||

||label/?h.aparc.DKTatlas.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*_exvivo.label label/?h.perirhinal_exvivo.label label/?h.entorhinal_exvivo.label ||