OtherUsefulFlags - Free Surfer Wiki

FreeSurfer Tutorial: Useful recon-all flags.

The following flags can be used in conjunction with individual steps or the entire process:

recon-all flag	Used with step	Input	Command Line	Output	Description
-autorecon-all
-all
-legacy
-clean-tal
-clean-seed
-clean-cp
-clean-bm
-clean-wm
-clean-aseg
-clean-wm
-clean-cpwm
-clean
-no-ca-align
-noaseg
-subcortseg	-gcareg	brainmask.mgz	["mri_em_register"] -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB40_talairach_2005-12-30.gca transforms/talairach.lta	transforms/talairach.lta	runs the subcortical segmentation and associated statistics
	-gcareg	nu.mgz		transforms/talairach.lta
	-canorm	brainmask.mgz	["mri_ca_normalize"] -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB40_talairach_2005-12-30.gca transforms/talairach.lta norm.mgz	norm.mgz
		nu.mgz
		transforms/talairach.lta
	-careg	brainmask.mgz	["mri_ca_register"] -align -mask brainmask.mgz -T transforms/talairach.lta norm.mgz $FREESURFER_HOME/average/RB40_talairach_2005-12-30.gca transforms/talairach.m3z	transforms/talairach.m3z
		transforms/talairach.lta
		norm.mgz
	-rmneck	nu.mgz	["mri_remove_neck"] -radius 25 nu.mgz transforms/talairach.m3z $FREESURFER_HOME/average/RB40_talairach_2005-12-30.gca nu_noneck.mgz	nu_noneck.mgz
	-rmneck	transforms/talairach.m3z		nu_noneck.mgz
	-skull-lta	transforms/talairach.lta	["mri_em_register"] -skull -t transforms/talairach.lta nu_noneck.mgz $FREESURFER_HOME/average/RB40_talairach_with_skull_2005-12-30.gca transforms/talairach_with_skull.lta	transforms/talairach_with_skull.lta
	-skull-lta	nu_noneck.mgz		transforms/talairach_with_skull.lta
	-calabel	norm.mgz	["mri_ca_label"] -align norm.mgz transforms/talairach.m3z $FREESURFER_HOME/average/RB40_talairach_2005-12-30.gca aseg.auto.mgz	aseg.auto.mgz
		transforms/talairach.m3z		aseg.auto.mgz
		aseg.auto.mgz	cp aseg.auto.mgz aseg.mgz	aseg.mgz
	-segstats	aseg.mgz	["mri_segstats"] --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --in mri/norm.mgz --ctab-default --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in-intensity-name orig --in-intensity-units MR --etiv --subject <subjid>	stats/aseg.stats
-cc-xyz <X Y Z>	-fill	wm.mgz	["mri_fill"] -a ../scripts/ponscc.cut.log -C X Y Z -xform transforms/talairach.xfm wm.mgz filled.mgz	filled.mgz	manually sets the corpus callosum seed point
-pons-xyz <X Y Z>	-fill	wm.mgz	["mri_fill"] -a ../scripts/ponscc.cut.log -P X Y Z -xform transforms/talairach.xfm wm.mgz filled.mgz	filled.mgz	manually sets the pons seed point
-rh-xyz <X Y Z>	-fill	wm.mgz	["mri_fill"] -a ../scripts/ponscc.cut.log -rh X Y Z -xform transforms/talairach.xfm wm.mgz filled.mgz	filled.mgz	manually sets the right hemisphere seed point
-lh-xyz <X Y Z>	-fill	wm.mgz	["mri_fill"] -a ../scripts/ponscc.cut.log -lh X Y Z -xform transforms/talairach.xfm wm.mgz filled.mgz	filled.mgz	manually sets the left hemisphere seed point
-old-atlas
	-gcareg	brain.mgz	["mri_em_register"] -mask brain.mgz -p .5 -fsamples fsamples.mgz nu.mgz $FREESURFER_HOME/average/talairach_mixed.gca transforms/talairach.lta	transforms/talairach.lta	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.
	-gcareg	nu.mgz		transforms/talairach.lta
	-canorm	brain.mgz	["mri_ca_normalize"] -mask brain.mgz nu.mgz $FREESURFER_HOME/average/talairach_mixed.gca transforms/talairach.lta norm.mgz	norm.mgz
		nu.mgz
		transforms/talairach.lta
	-careg	brain.mgz	["mri_ca_register"] -cross-sequence -mask brain.mgz -T transforms/talairach.lta norm.mgz $FREESURFER_HOME/average/talairach_mixed.gca transforms/talairach.m3z	transforms/talairach.m3z
		transforms/talairach.lta
		norm.mgz
	-calabel	norm.mgz	["mri_ca_label"] -cross-sequence norm.mgz transforms/talairach.m3z $FREESURFER_HOME/average/talairach_mixed.gca aseg.mgz	aseg.mgz
	-calabel	transforms/talairach.m3z		aseg.mgz
	-surfreg	?h.sphere	["mris_register"] -w 0 -curv ?h.sphere $FREESURFER_HOME/average?h.average.tif ?h.sphere.reg	?h.sphere.reg
	-contrasurfreg	rh.sphere	["mris_register"] -w 0 -curv -reverse rh.sphere $FREESURFER_HOME/average?h.average.tif rh.lh.sphere.reg	rh.lh.sphere.reg
	-contrasurfreg	lh.sphere	["mris_register"] -w 0 -curv -reverse lh.sphere $FREESURFER_HOME/average?h.average.tif lh.rh.sphere.reg	lh.rh.sphere.reg
	-avgcurv	?h.sphere.reg	["mrisp_paint"] -a 5 $FREESURFER_HOME/average?h.average.tif ?h.sphere.reg ?h.avg_curv	?h.avg_curv
	-cortparc	?h.sphere.reg	["mris_ca_label"] -t $CPAnnotTable subj ?h sphere.reg $FREESURFER_HOME/average/?h.atlas2002_simple.gcs ?h.aparc.annot	label/?h.aparc.annot
-deface		orig.mgz	mri_deface orig.mgz $FREESURFER_HOME/average/talairach_mixed_with_skull.gca $FREESURFER_HOME/average/face.gca orig_defaced.mgz	orig_defaced.mgz	removes the face from the orig volume to anonymize it.

The following flags can be used after certain manual intervention to regenerate accurate volumes and surfaces:

recon-all step	Individual Flag	Input	Command Line	Output
["recon-all"] -autorecon2-cp -subjid subj (use this after setting control points. This flag will preserve your wm.mgz edits and remake all necessary volumes and surfaces)
	-normalization2	brain.mgz	["mri_normalize"] -f $SUBJECTS_DIR/subjid/tmp/control.dat -mask brain.mgz nu.mgz T1.mgz	T1.mgz
		nu.mgz		T1.mgz
		T1.mgz	["mri_mask"] T1.mgz brain.mgz brain.mgz	brain.mgz
		brain.mgz	["mri_mask"] T1.mgz brain.mgz brain.mgz	brain.mgz
	-segmentation	brain.mgz	["mri_segment"] -keep brain.mgz wm.mgz	wm.mgz
	-edit_wm_with_aseg	wm.mgz	["mri_edit_wm_with_aseg"] wm.mgz aseg.mgz wm.mgz	wm.mgz
	-edit_wm_with_aseg	aseg.mgz	["mri_edit_wm_with_aseg"] wm.mgz aseg.mgz wm.mgz	wm.mgz
	-fill	wm.mgz	["mri_fill"] -a ../scripts/ponscc.cut.log -xform transforms/talairach.xfm -segmentation aseg.mgz wm.mgz filled.mgz	filled.mgz
	-fill	aseg.mgz		../scripts/ponscc.cut.log
	-tessellate	filled.mgz	["mri_tessellate"] filled.mgz 255 ../surf/lh.orig	lh.orig
	-tessellate	filled.mgz	["mri_tessellate"] filled.mgz 128 ../surf/rh.orig	rh.orig
	-smooth1	?h.orig	["mris_smooth"] ?h.orig ?h.smoothwm	?h.smoothwm
	-inflate1	?h.smoothwm	["mris_inflate"] ?h.smoothwm ?h.inflated	?h.inflated
	-qsphere	?h.inflated	["mris_sphere"] -w 0 -inflate -in 200 -q ?h.inflated ?h.qsphere	?h.qsphere
	-fix	?h.qsphere	["mris_fix_topology"] subj ?h	?h.orig
	-euler	?h.orig	["mris_euler_number"] ?h.orig	?h.orig.euler
	-smooth2	?h.orig	["mris_smooth"] ?h.orig ?h.smoothwm	?h.smoothwm
	-inflate2	?h.smoothwm	["mris_inflate"] ?h.smoothwm ?h.inflated	?h.inflated
	-finalsurfs	brain.mgz	["mris_make_surfaces"] -w 0 subj ?h	?h.white
		?h.orig		?h.pial
		?h.orig		?h.thickness
	-cortribbon	orig.mgz	["mri_surf2vol"] --mkmask --hemi ?h --fillribbon --template orig.mgz --volregidentity subj --outvol ?h.ribbon.mgz	?h.ribbon.mgz
		?h.white
		?h.pial

recon-all step	Individual Flag	Input	Command Line	Output
["recon-all"] -autorecon2-wm -subjid subj (use this after doing manual wm edits. This flag will regenerate all necessary volumes and surfaces)
	-fill	wm.mgz	["mri_fill"] -a ../scripts/ponscc.cut.log -xform transforms/talairach.xfm -segmentation aseg.mgz wm.mgz filled.mgz	filled.mgz
	-fill	aseg.mgz		../scripts/ponscc.cut.log
	-tessellate	filled.mgz	["mri_tessellate"] filled.mgz 255 ../surf/lh.orig	lh.orig
	-tessellate	filled.mgz	["mri_tessellate"] filled.mgz 128 ../surf/rh.orig	rh.orig
	-smooth1	?h.orig	["mris_smooth"] ?h.orig ?h.smoothwm	?h.smoothwm
	-inflate1	?h.smoothwm	["mris_inflate"] ?h.smoothwm ?h.inflated	?h.inflated
	-qsphere	?h.inflated	["mris_sphere"] -w 0 -inflate -in 200 -q ?h.inflated ?h.qsphere	?h.qsphere
	-fix	?h.qsphere	["mris_fix_topology"] subj ?h	?h.orig
	-euler	?h.orig	["mris_euler_number"] ?h.orig	?h.orig.euler
	-smooth2	?h.orig	["mris_smooth"] ?h.orig ?h.smoothwm	?h.smoothwm
	-inflate2	?h.smoothwm	["mris_inflate"] ?h.smoothwm ?h.inflated	?h.inflated
	-finalsurfs	brain.mgz	["mris_make_surfaces"] -w 0 subj ?h	?h.white
		?h.orig		?h.pial
		?h.orig		?h.thickness
	-cortribbon	orig.mgz	["mri_surf2vol"] --mkmask --hemi ?h --fillribbon --template orig.mgz --volregidentity subj --outvol ?h.ribbon.mgz	?h.ribbon.mgz
		?h.white
		?h.pial

recon-all step	Individual Flag	Input	Command Line	Output
["recon-all"] -autorecon2-pial -subjid subj (use this after editing brain.mgz to alter pial surface. This flag will regenerate all final surfaces)
	-finalsurfs	brain.mgz	["mris_make_surfaces"] -w 0 subj ?h	?h.white
		?h.orig		?h.pial
				?h.thickness
	-cortribbon	orig.mgz	["mri_surf2vol"] --mkmask --hemi ?h --fillribbon --template orig.mgz --volregidentity subj --outvol ?h.ribbon.mgz	?h.ribbon.mgz
		?h.white
		?h.pial