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
-dontrun	useful for debugging. just prints the commands that will run (does not execute them).
-legacy	use this flag on data that was previously processed with a different version of freesurfer. Use this flag THE FIRST TIME only. It will automatically keep all your prior edits (talairach, control points, white matter etc).
-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	use this flag to clear all of your manual edits and run it completely fresh.
-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.

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-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
-jacobian_dist0		?h.sphere.reg	mris_register -curv -norot -jacobian ../surf/lh.jacobian -dist 0 ../surf/lh.sphere.reg $FREESURFER_HOME/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.dist0.jacobian.reg	?h.jacobian_dist0	Computes how much an individual surface must be distorted in order to perfectly match the atlas (ie, distance contraints are turned off).
-jacobian_dist0		?h.sphere.reg		?h.sphere.jacobian.reg
-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 (if a data set has or needs spherical morphing, add the -autorecon3 flag):

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	brainmask.mgz	["mri_normalize"] -mask brainmask.mgz norm.mgz brain.mgz	brain.mgz
		norm.mgz
		brain.mgz	["mri_mask"] 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.mgz wm.asegedit.mgz	wm.asegedit.mgz
		aseg.mgz
		brain.mgz
		wm.asegedit.mgz	["mri_pretess"] wm.asegedit.mgz norm.mgz wm.mgz	wm.mgz
		norm.mgz
	-fill	wm.mgz	["mri_fill"] -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.mgz wm.mgz filled.mgz	filled.mgz
		aseg.mgz		../scripts/ponscc.cut.log
		transforms/talairach.lta
	-tessellate	filled.mgz	["mri_tessellate"] filled.mgz 255 ../surf/lh.orig.nofix	lh.orig.nofix
			["mri_tessellate"] filled.mgz 127 ../surf/rh.orig.nofix	rh.orig.nofix
	-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 -0 ?h.inflated.nofix ?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"] -errors -mgz -sphere qsphere.nofix -ga <subjid> ?h	?h.orig
	-finalsurfs	brain.finalsurfs.mgz	["mris_make_surfaces"] -mgz -w 0 -T1 brain.finalsurfs.mgz subj ?h	?h.white
				?h.pial
				?h.thickness
		?h.orig
				?h.curv
				?h.area
	-smooth2	?h.white	["mris_smooth"] ?h.white ?h.smoothwm	?h.smoothwm
	-inflate2	?h.white	["mris_inflate"] ?h.white ?h.inflated	?h.inflated
				?h.sulc
	-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.lta -segmentation aseg.mgz wm.mgz filled.mgz	filled.mgz
		aseg.mgz		../scripts/ponscc.cut.log
		transforms/talairach.lta		../scripts/ponscc.cut.log
	-tessellate	filled.mgz	["mri_tessellate"] filled.mgz 255 ../surf/lh.orig.nofix	lh.orig.nofix
	-tessellate	filled.mgz	["mri_tessellate"] filled.mgz 127 ../surf/rh.orig.nofix	rh.orig.nofix
	-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 -0 ?h.inflated.nofix ?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"] -errors -mgz -sphere qsphere.nofix -ga <subjid> ?h	?h.orig
	-finalsurfs	brain.finalsurfs.mgz	["mris_make_surfaces"] -mgz -w 0 -T1 brain.finalsurfs.mgz subj ?h	?h.white
				?h.pial
				?h.thickness
		?h.orig
				?h.curv
				?h.area
	-smooth2	?h.white	["mris_smooth"] ?h.white ?h.smoothwm	?h.smoothwm
	-inflate2	?h.white	["mris_inflate"] ?h.white ?h.inflated	?h.inflated
	-inflate2	?h.white	["mris_inflate"] ?h.white ?h.inflated	?h.sulc
	-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.finalsurfs.mgz	["mris_make_surfaces"] -mgz -w 0 -T1 brain.finalsurfs.mgz subj ?h	?h.white
				?h.pial
				?h.thickness
		?h.orig
				?h.curv
				?h.area
	-smooth2	?h.white	["mris_smooth"] ?h.white ?h.smoothwm	?h.smoothwm
	-inflate2	?h.white	["mris_inflate"] ?h.white ?h.inflated	?h.inflated
				?h.sulc
	-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-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)
	-tessellate	filled.mgz	["mri_tessellate"] filled.mgz 255 ../surf/lh.orig.nofix	lh.orig.nofix
	-tessellate	filled.mgz	["mri_tessellate"] filled.mgz 127 ../surf/rh.orig.nofix	rh.orig.nofix
	-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 -0 ?h.inflated.nofix ?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"] -errors -mgz -sphere qsphere.nofix -ga <subjid> ?h	?h.orig
	-finalsurfs	brain.finalsurfs.mgz	["mris_make_surfaces"] -mgz -w 0 -T1 brain.finalsurfs.mgz subj ?h	?h.white
				?h.pial
				?h.thickness
		?h.orig
				?h.curv
				?h.area
	-smooth2	?h.white	["mris_smooth"] ?h.white ?h.smoothwm	?h.smoothwm
	-inflate2	?h.white	["mris_inflate"] ?h.white ?h.inflated	?h.inflated
	-inflate2	?h.white	["mris_inflate"] ?h.white ?h.inflated	?h.sulc
	-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

-  ⇤ ← Revision 5 as of 2005-10-18 12:13:14 → 
  Size: 9055
  Editor: JenniPacheco
  Comment:
+   ← Revision 59 as of 2008-02-11 17:34:05 → ⇥
  Size: 19663
  Editor: AllisonStevens
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
+#acl AdminGroup:read,write,delete,revert All:read
-Line 3:
+Line 5:
+This page extends ReconAllDevTable.
-Line 5:
+Line 8:
-||<rowbgcolor='#80FF80'>'''recon-all flag'''||'''Used with step'''||'''Input'''||'''Command Line'''||'''Output'''||'''Description'''||
||<bgcolor='#FFFFE0'>-usecontrolpoints||<bgcolor='#FFFFE0'>-normalization||<bgcolor='#E0E0FF'>nu.mgz||<bgcolor='#E0E0FF'>["mri_normalize"] -f $SUBJECTS_DIR/subjid/tmp/control.dat nu.mgz T1.mgz||<bgcolor='#E0E0FF'>T1.mgz||<bgcolor='#FFFFE0'>uses control points, saved to tmp/control.dat to modify the normalization||
||<bgcolor='#FFFFE0'>-keepwmedits||<bgcolor='#FFFFE0'>-segmentation||<bgcolor='#E0E0FF'>brain.mgz||<bgcolor='#E0E0FF'>["mri_segment"] -keep brain.mgz wm.mgz||<bgcolor='#E0E0FF'>wm.mgz||<bgcolor='#FFFFE0'>preserves any previous edits to wm volume||
||<bgcolor='#FFFFE0'>-cc-xyz <X Y Z>||<bgcolor='#FFFFE0'>-fill||<bgcolor='#E0E0FF'>wm.mgz||<bgcolor='#E0E0FF'>["mri_fill"] -a ../scripts/ponscc.cut.log -C X Y Z -xform transforms/talairach.xfm wm.mgz filled.mgz||<bgcolor='#E0E0FF'>filled.mgz||<bgcolor='#FFFFE0'>manually sets the corpus callosum seed point||
||<bgcolor='#FFFFE0'>-pons-xyz <X Y Z>||<bgcolor='#FFFFE0'>-fill||<bgcolor='#E0E0FF'>wm.mgz||<bgcolor='#E0E0FF'>["mri_fill"] -a ../scripts/ponscc.cut.log -P X Y Z -xform transforms/talairach.xfm wm.mgz filled.mgz||<bgcolor='#E0E0FF'>filled.mgz||<bgcolor='#FFFFE0'>manually sets the pons seed point||
||<bgcolor='#FFFFE0'>-rh-xyz <X Y Z>||<bgcolor='#FFFFE0'>-fill||<bgcolor='#E0E0FF'>wm.mgz||<bgcolor='#E0E0FF'>["mri_fill"] -a ../scripts/ponscc.cut.log -rh X Y Z -xform transforms/talairach.xfm wm.mgz filled.mgz||<bgcolor='#E0E0FF'>filled.mgz||<bgcolor='#FFFFE0'>manually sets the right hemisphere seed point||
||<bgcolor='#FFFFE0'>-lh-xyz <X Y Z>||<bgcolor='#FFFFE0'>-fill||<bgcolor='#E0E0FF'>wm.mgz||<bgcolor='#E0E0FF'>["mri_fill"] -a ../scripts/ponscc.cut.log -lh X Y Z -xform transforms/talairach.xfm wm.mgz filled.mgz||<bgcolor='#E0E0FF'>filled.mgz||<bgcolor='#FFFFE0'>manually sets the left hemisphere seed point||
||<bgcolor='#FFFFE0'>-old-atlas||<bgcolor='#FFFFE0'>||<bgcolor='#E0E0FF'>||<bgcolor='#E0E0FF'>||<bgcolor='#E0E0FF'>||<bgcolor='#FFFFE0'>||
||<bgcolor='#FFFFE0'>-rerun||<bgcolor='#FFFFE0'>||<bgcolor='#E0E0FF'>||<bgcolor='#E0E0FF'>||<bgcolor='#E0E0FF'>||<bgcolor='#FFFFE0'>||
+||<bgcolor='#FFFFE0'>'''-autorecon-all'''||<|2-5(bgcolor='#E0E0FF'>either of these flags will work to run the entire recon-all process.||
||<bgcolor='#FFFFE0'>'''-all'''||
||<bgcolor='#FFFFE0'>'''-dontrun'''||<-5(bgcolor='#E0E0FF'>useful for debugging. just prints the commands that will run (does not execute them).||
||<bgcolor='#FFFFE0'>'''-legacy'''||<-5(bgcolor='#E0E0FF'>use this flag on data that was previously processed with a different version of freesurfer.  Use this flag THE FIRST TIME only.  It will automatically keep all your prior edits (talairach, control points, white matter etc). ||
||<bgcolor='#FFFFE0'>'''-clean-tal'''||<-5(bgcolor='#E0E0FF'>trashes any manual edits to the talairach, makes talairach.xfm and talairach.auto.xfm the same and runs using the automatically generated talairach.xfm||
||<bgcolor='#FFFFE0'>'''-clean-seed'''||<-5(bgcolor='#E0E0FF'>trashes all saved seed point for the cutting planes and uses the automatically set cutting planes.||
||<bgcolor='#FFFFE0'>'''-clean-cp'''||<-5(bgcolor='#E0E0FF'>trashes control points and runs the normalization without control points.||
||<bgcolor='#FFFFE0'>'''-clean-bm'''||<-5(bgcolor='#E0E0FF'>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||
||<bgcolor='#FFFFE0'>'''-clean-wm'''||<-5(bgcolor='#E0E0FF'>trashes any manual edits to the wm.mgz volume and runs using the automatically generated wm.mgz.||
||<bgcolor='#FFFFE0'>'''-clean-aseg'''||<-5(bgcolor='#E0E0FF'>trashes any manual edits to the aseg.mgz and runs using the automatically generated aseg.mgz||
||<bgcolor='#FFFFE0'>'''-clean-cpwm'''||<-5(bgcolor='#E0E0FF'>combination of -clean-cp and -clean-wm.||
||<bgcolor='#FFFFE0'>'''-clean'''||<-5(bgcolor='#E0E0FF'>use this flag to clear all of your manual edits and run it completely fresh.||
||<bgcolor='#FFFFE0'>'''-noaseg'''||<-5(bgcolor='#E0E0FF'>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.||
||<bgcolor='#FFFFE0'>'''-norandomness'''||<-5(bgcolor='#E0E0FF'>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.||
-Line 15:
+Line 23:
-The following flags can be used after certain manual intervention to regenerate accurate volumes and surfaces:
+||<rowbgcolor='#80FF80'>'''recon-all flag'''||'''Used with step'''||'''Description'''||
||<|2(bgcolor='#FFFFE0'>'''-no-ca-align'''||<bgcolor='#FFFFE0'>-careg||<|2(bgcolor='#FFFFE0'>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.||
||<bgcolor='#FFFFE0'>-calabel||
||<|7(bgcolor='#FFFFE0'>'''-subcortseg'''||<bgcolor='#FFFFE0'>-gcareg||<|7(bgcolor='#FFFFE0'>runs the subcortical segmentation and associated statistics||
||<bgcolor='#FFFFE0'>-canorm||
||<bgcolor='#FFFFE0'>-careg||
||<bgcolor='#FFFFE0'>-rmneck||
||<bgcolor='#FFFFE0'>-skull-lta||
||<bgcolor='#FFFFE0'>-calabel||
||<bgcolor='#FFFFE0'>-segstats||
||<bgcolor='#FFFFE0'>'''-cc-xyz <X Y Z>'''||<bgcolor='#FFFFE0'>-fill||<bgcolor='#E0E0FF'>wm.mgz||<bgcolor='#E0E0FF'>["mri_fill"] -a ../scripts/ponscc.cut.log -C X Y Z -xform transforms/talairach.xfm wm.mgz filled.mgz||<bgcolor='#E0E0FF'>filled.mgz||<bgcolor='#FFFFE0'>manually sets the corpus callosum seed point||
||<bgcolor='#FFFFE0'>'''-pons-xyz <X Y Z>'''||<bgcolor='#FFFFE0'>-fill||<bgcolor='#E0E0FF'>wm.mgz||<bgcolor='#E0E0FF'>["mri_fill"] -a ../scripts/ponscc.cut.log -P X Y Z -xform transforms/talairach.xfm wm.mgz filled.mgz||<bgcolor='#E0E0FF'>filled.mgz||<bgcolor='#FFFFE0'>manually sets the pons seed point||
||<bgcolor='#FFFFE0'>'''-rh-xyz <X Y Z>'''||<bgcolor='#FFFFE0'>-fill||<bgcolor='#E0E0FF'>wm.mgz||<bgcolor='#E0E0FF'>["mri_fill"] -a ../scripts/ponscc.cut.log -rh X Y Z -xform transforms/talairach.xfm wm.mgz filled.mgz||<bgcolor='#E0E0FF'>filled.mgz||<bgcolor='#FFFFE0'>manually sets the right hemisphere seed point||
||<bgcolor='#FFFFE0'>'''-lh-xyz <X Y Z>'''||<bgcolor='#FFFFE0'>-fill||<bgcolor='#E0E0FF'>wm.mgz||<bgcolor='#E0E0FF'>["mri_fill"] -a ../scripts/ponscc.cut.log -lh X Y Z -xform transforms/talairach.xfm wm.mgz filled.mgz||<bgcolor='#E0E0FF'>filled.mgz||<bgcolor='#FFFFE0'>manually sets the left hemisphere seed point||
||<|2(bgcolor='#FFFFE0'>'''-jacobian_dist0'''||<|2(bgcolor='#FFFFE0'> ||<|2(bgcolor='#E0E0FF'>?h.sphere.reg||<|2(bgcolor='#E0E0FF'>mris_register -curv -norot -jacobian ../surf/lh.jacobian -dist 0 ../surf/lh.sphere.reg $FREESURFER_HOME/average/lh.average.curvature.filled.buckner40.tif  ../surf/lh.sphere.dist0.jacobian.reg||<bgcolor='#E0E0FF'>?h.jacobian_dist0||<|2(bgcolor='#FFFFE0'>Computes how much an individual surface must be distorted in order to perfectly match the atlas (ie, distance contraints are turned off). ||
||<rowbgcolor='#E0E0FF'>?h.sphere.jacobian.reg||
||<|16(bgcolor='#FFFFE0'>'''-old-atlas'''||
||<|2(bgcolor='#FFFFE0'>-gcareg||<bgcolor='#E0E0FF'>brain.mgz||<|2(bgcolor='#E0E0FF'>["mri_em_register"] -mask brain.mgz -p .5 -fsamples fsamples.mgz nu.mgz $FREESURFER_HOME/average/talairach_mixed.gca transforms/talairach.lta||<|2(bgcolor='#E0E0FF'>transforms/talairach.lta||<|15(bgcolor='#FFFFE0'>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.||
||<rowbgcolor='#E0E0FF'>nu.mgz||
||<|3(bgcolor='#FFFFE0'>-canorm||<bgcolor='#E0E0FF'>brain.mgz||<|3(bgcolor='#E0E0FF'>["mri_ca_normalize"] -mask brain.mgz nu.mgz $FREESURFER_HOME/average/talairach_mixed.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 $FREESURFER_HOME/average/talairach_mixed.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 $FREESURFER_HOME/average/talairach_mixed.gca aseg.mgz||<|2(bgcolor='#E0E0FF'>aseg.mgz||
||<rowbgcolor='#E0E0FF'>transforms/talairach.m3z||
||<bgcolor='#FFFFE0'>-surfreg||<bgcolor='#E0E0FF'>?h.sphere||<bgcolor='#E0E0FF'>["mris_register"] -w 0 -curv ?h.sphere $FREESURFER_HOME/average?h.average.tif ?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 $FREESURFER_HOME/average?h.average.tif rh.lh.sphere.reg||<bgcolor='#E0E0FF'>rh.lh.sphere.reg||
||<rowbgcolor='#E0E0FF'>lh.sphere||["mris_register"] -w 0 -curv -reverse lh.sphere $FREESURFER_HOME/average?h.average.tif lh.rh.sphere.reg||lh.rh.sphere.reg||
||<bgcolor='#FFFFE0'>-avgcurv||<bgcolor='#E0E0FF'>?h.sphere.reg||<bgcolor='#E0E0FF'>["mrisp_paint"] -a 5 $FREESURFER_HOME/average?h.average.tif ?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 $FREESURFER_HOME/average/?h.atlas2002_simple.gcs ?h.aparc.annot||<bgcolor='#E0E0FF'>label/?h.aparc.annot||
||<bgcolor='#FFFFE0'>'''-deface'''||<bgcolor='#FFFFE0'>||<bgcolor='#E0E0FF'>orig.mgz||<bgcolor='#E0E0FF'>mri_deface orig.mgz $FREESURFER_HOME/average/talairach_mixed_with_skull.gca $FREESURFER_HOME/average/face.gca orig_defaced.mgz||<bgcolor='#E0E0FF'>orig_defaced.mgz||<bgcolor='#FFFFE0'>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 (if a data set has or needs spherical morphing, add the -autorecon3 flag):
-Line 18:
+Line 60:
-||<|25(bgcolor='#FFFFE0'>["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)||
||<|4(bgcolor='#FFFFE0'>-normalization2||<bgcolor='#E0E0FF'>brain.mgz||<|2(bgcolor='#E0E0FF'>["mri_normalize"] -f $SUBJECTS_DIR/subjid/tmp/control.dat -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||
+||<|34(bgcolor='#FFFFE0'>'''["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)||
||<|4(bgcolor='#FFFFE0'>-normalization2||<bgcolor='#E0E0FF'>brainmask.mgz||<|2(bgcolor='#E0E0FF'>["mri_normalize"] -mask brainmask.mgz norm.mgz brain.mgz||<|2(bgcolor='#E0E0FF'>brain.mgz||
||<rowbgcolor='#E0E0FF'>norm.mgz||
||<rowbgcolor='#E0E0FF'>brain.mgz||<|2(>["mri_mask"] brain.mgz brainmask.mgz brain.finalsurfs.mgz||<|2(>brain.finalsurfs.mgz||
||<rowbgcolor='#E0E0FF'>brainmask.mgz||
||<|6(bgcolor='#FFFFE0'>-segmentation||<bgcolor='#E0E0FF'>brain.mgz||<bgcolor='#E0E0FF'>["mri_segment"] brain.mgz wm.seg.mgz||<bgcolor='#E0E0FF'>wm.seg.mgz||
||<bgcolor='#E0E0FF'>wm.seg.mgz||<|3(bgcolor='#E0E0FF'>["mri_edit_wm_with_aseg"] wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz||<|3(bgcolor='#E0E0FF'>wm.asegedit.mgz||
||<rowbgcolor='#E0E0FF'>aseg.mgz||
-Line 23:
+Line 69:
-||<bgcolor='#FFFFE0'>-segmentation||<bgcolor='#E0E0FF'>brain.mgz||<bgcolor='#E0E0FF'>["mri_segment"] -keep 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 128 ../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||
+||<bgcolor='#E0E0FF'>wm.asegedit.mgz||<|2(bgcolor='#E0E0FF'>["mri_pretess"] wm.asegedit.mgz norm.mgz wm.mgz||<|2(bgcolor='#E0E0FF'>wm.mgz||
||<rowbgcolor='#E0E0FF'>norm.mgz||
||<|3(bgcolor='#FFFFE0'>-fill||<bgcolor='#E0E0FF'>wm.mgz||<|3(bgcolor='#E0E0FF'>["mri_fill"] -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.mgz wm.mgz filled.mgz||<bgcolor='#E0E0FF'>filled.mgz||
||<rowbgcolor='#E0E0FF'>aseg.mgz||<|2(bgcolor='#E0E0FF'>../scripts/ponscc.cut.log||
||<rowbgcolor='#E0E0FF'>transforms/talairach.lta||
||<|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||
||<|6(bgcolor='#FFFFE0'>-finalsurfs||<|3(bgcolor='#E0E0FF'>brain.finalsurfs.mgz||<|6(bgcolor='#E0E0FF'>["mris_make_surfaces"] -mgz -w 0 -T1 brain.finalsurfs.mgz subj ?h||<bgcolor='#E0E0FF'>?h.white||
||<rowbgcolor='#E0E0FF'>?h.pial||
-Line 40:
+Line 85:
+||<|3(rowbgcolor='#E0E0FF'>?h.orig||
||<rowbgcolor='#E0E0FF'>?h.curv||
||<rowbgcolor='#E0E0FF'>?h.area||
||<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||
||<|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||

||<rowbgcolor='#80FF80'>'''recon-all step'''||'''Individual Flag'''||'''Input'''||'''Command Line'''||'''Output'''||
||<|24(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.mgz wm.mgz filled.mgz||<bgcolor='#E0E0FF'>filled.mgz||
||<rowbgcolor='#E0E0FF'>aseg.mgz||<|2(bgcolor='#E0E0FF'>../scripts/ponscc.cut.log||
||<rowbgcolor='#E0E0FF'>transforms/talairach.lta||
||<|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||
||<|6(bgcolor='#FFFFE0'>-finalsurfs||<|3(bgcolor='#E0E0FF'>brain.finalsurfs.mgz||<|6(bgcolor='#E0E0FF'>["mris_make_surfaces"] -mgz -w 0 -T1 brain.finalsurfs.mgz subj ?h||<bgcolor='#E0E0FF'>?h.white||
||<rowbgcolor='#E0E0FF'>?h.pial||
||<rowbgcolor='#E0E0FF'>?h.thickness||
||<|3(rowbgcolor='#E0E0FF'>?h.orig||
||<rowbgcolor='#E0E0FF'>?h.curv||
||<rowbgcolor='#E0E0FF'>?h.area||
||<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||
-Line 46:
+Line 123:
-||<|18(bgcolor='#FFFFE0'>["recon-all"] -autorecon2-wm -subjid subj (use this after doing manual wm edits.  This flag will regenerate all necessary volumes and surfaces)||
||<|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 128 ../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||
+||<|13(bgcolor='#FFFFE0'>'''["recon-all"] -autorecon2-pial -subjid subj '''(use this after editing brain.mgz to alter pial surface.  This flag will regenerate all final surfaces)||
||<|6(bgcolor='#FFFFE0'>-finalsurfs||<|3(bgcolor='#E0E0FF'>brain.finalsurfs.mgz||<|6(bgcolor='#E0E0FF'>["mris_make_surfaces"] -mgz -w 0 -T1 brain.finalsurfs.mgz subj ?h||<bgcolor='#E0E0FF'>?h.white||
||<rowbgcolor='#E0E0FF'>?h.pial||
-Line 61:
+Line 127:
+||<|3(rowbgcolor='#E0E0FF'>?h.orig||
||<rowbgcolor='#E0E0FF'>?h.curv||
||<rowbgcolor='#E0E0FF'>?h.area||
||<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||
-Line 66:
+Line 138:
-||<|6(bgcolor='#FFFFE0'>["recon-all"] -autorecon2-pial -subjid subj (use this after editing brain.mgz to alter pial surface.  This flag will regenerate all final surfaces)||
||<|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||
+||<|21(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||
||<|6(bgcolor='#FFFFE0'>-finalsurfs||<|3(bgcolor='#E0E0FF'>brain.finalsurfs.mgz||<|6(bgcolor='#E0E0FF'>["mris_make_surfaces"] -mgz -w 0 -T1 brain.finalsurfs.mgz subj ?h||<bgcolor='#E0E0FF'>?h.white||
||<rowbgcolor='#E0E0FF'>?h.pial||
-Line 70:
+Line 150:
+||<|3(rowbgcolor='#E0E0FF'>?h.orig||
||<rowbgcolor='#E0E0FF'>?h.curv||
||<rowbgcolor='#E0E0FF'>?h.area||
||<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||
-Line 73:
+Line 159: