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).
-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
-clean-cw256
-clean-lta
-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.
-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
-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.
-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.
-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.
-deface	removes the face from the orig volume to anonymize it.
-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-xyz <X Y Z>	-fill	manually sets the corpus callosum seed point
-pons-xyz <X Y Z>	-fill	manually sets the pons seed point
-rh-xyz <X Y Z>	-fill	manually sets the right hemisphere seed point
-lh-xyz <X Y Z>	-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).
-old-atlas
	-gcareg	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.
	-canorm
	-careg
	-calabel
	-surfreg
	-contrasurfreg
	-avgcurv
	-cortparc

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-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.auto_noCCseg.mgz wm.mgz filled.mgz	filled.mgz
		aseg.auto_noCCseg.mgz		../scripts/ponscc.cut.log
		transforms/talairach.lta		../scripts/ponscc.cut.log
	-tessellate	filled.mgz	mri_pretess filled.mgz 255 norm.mgz filled-pretess255.mgz	filled-pretess255.mgz
		norm.mgz	mri_pretess filled.mgz 255 norm.mgz filled-pretess255.mgz	filled-pretess255.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	mri_pretess filled.mgz 127 norm.mgz filled-pretess127.mgz	filled-pretess127.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 -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 -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.mgz, brain.finalsurfs.mgz, wm.mgz, filled.mgz	mris_make_surfaces -whiteonly -noaparc -mgz -T1 brain.finalsurfs <subjid> ?h	?h.white
		?h.orig
				?h.curv
				?h.area
				?h.cortex.label
	(bgcolor='#FFFFE0'>-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.smoothwm	mris_inflate ?h.smoothwm ?h.inflated	?h.sulc
		?h.inflated	mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ?h.inflated	?h.inflated.H
?h.inflated.K		?h.inflated

recon-all step	Individual Flag	Input	Command Line	Output
recon-all -autorecon2-noaseg -subjid subj (use this after doing manual edits to the aseg. This flag will regenerate all final surfaces)
	-normalization2	brainmask.mgz	mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz	brain.mgz
		norm.mgz
		aseg.mgz
	-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.finalsurfs.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 1 as of 2005-10-18 11:45:29 → 
  Size: 15095
  Editor: JenniPacheco
  Comment:
+   ← Revision 108 as of 2011-12-06 19:11:35 → ⇥
  Size: 17812
  Editor: KhoaNguyen
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
+#acl AdminGroup:read,write,delete,revert  KhoaNguyen:read,write,delete,revert All:read
-Line 3:
+Line 5:
+This page extends ReconAllDevTable.
The following flags can be used in conjunction with individual steps or the entire process:
-Line 4:
+Line 8:
-||<rowbgcolor='#80FF80'>'''recon-all flag'''||'''Used with step'''||'''Input'''||'''Command Line'''||'''Output'''||
||<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||
||<|10(bgcolor='#FFFFE0'>["recon-all"] -autorecon1 -subjid subj||
||<|3(bgcolor='#FFFFE0'>-motioncor||<bgcolor='#E0E0FF'>orig/001.mgz||<|2(bgcolor='#E0E0FF'>["mri_motion_correct2"] -i orig/001.mgz -i orig/002.mgz -o rawavg.mgz||<|2(bgcolor='#E0E0FF'>rawavg.mgz||
||<rowbgcolor='#E0E0FF'>orig/002.mgz||
||<rowbgcolor='#E0E0FF'>rawavg.mgz||["mri_convert"] rawavg.mgz orig.mgz --conform||orig.mgz||
||<|3(bgcolor='#FFFFE0'>-nuintensitycor||<bgcolor='#E0E0FF'>orig.mgz||<bgcolor='#E0E0FF'>["mri_convert"] orig.mgz orig.mnc||<bgcolor='#E0E0FF'>orig.mnc||
||<rowbgcolor='#E0E0FF'>orig.mnc||(4 iterations of) ["nu_correct"] -clobber nu0.mnc nu1.mnc||nu4.mnc||
||<rowbgcolor='#E0E0FF'>nu4.mnc||["mri_convert"] nu4.mnc nu.mgz||nu.mgz||
||<bgcolor='#FFFFE0'>-talairach||<bgcolor='#E0E0FF'>nu.mgz||<bgcolor='#E0E0FF'>["talairach2"] subjid -mgz||<bgcolor='#E0E0FF'>transforms/talairach.xfm||
||<bgcolor='#FFFFE0'>-normalization||<bgcolor='#E0E0FF'>nu.mgz||<bgcolor='#E0E0FF'>["mri_normalize"] nu.mgz T1.mgz||<bgcolor='#E0E0FF'>T1.mgz||
||<bgcolor='#FFFFE0'>-skullstrip||<bgcolor='#E0E0FF'>T1.mgz||<bgcolor='#E0E0FF'>["mri_watershed"] T1.mgz brain.mgz||<bgcolor='#E0E0FF'>brain.mgz||
||<-5(rowbgcolor='#FF8080'>Check skullstrip (brain.mgz), talairach (transforms/talairach.xfm), and normalization (brain.mgz or T1.mgz - mean wm voxel value = 110)||
||<|36(bgcolor='#FFFFE0'>["recon-all"] -autorecon2 -subjid subj||
||<|2(bgcolor='#FFFFE0'>-gcareg||<bgcolor='#E0E0FF'>brain.mgz||<|2(bgcolor='#E0E0FF'>["mri_em_register"] -mask brain.mgz -p .5 -fsamples fsamples.mgz nu.mgz $GCA transforms/talairach.lta||<|2(bgcolor='#E0E0FF'>transforms/talairach.lta||
||<rowbgcolor='#E0E0FF'>nu.mgz||
||<|3(bgcolor='#FFFFE0'>-canorm||<bgcolor='#E0E0FF'>brain.mgz||<|3(bgcolor='#E0E0FF'>["mri_ca_normalize"] -mask brain.mgz nu.mgz $GCA transforms/talairach.lta norm.mgz||<|3(bgcolor='#E0E0FF'>norm.mgz||
||<rowbgcolor='#E0E0FF'>nu.mgz||
+||<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-xopts'''||<-5(bgcolor='#E0E0FF'>||
||<bgcolor='#FFFFE0'>'''-clean-cw256'''||<-5(bgcolor='#E0E0FF'>||
||<bgcolor='#FFFFE0'>'''-clean-lta'''||<-5(bgcolor='#E0E0FF'>||
||<bgcolor='#FFFFE0'>'''-clean-pfh'''||<-5(bgcolor='#E0E0FF'> trashes preflood height volumes (skullstrip)||
||<bgcolor='#FFFFE0'>'''-clean-bfse'''||<-5(bgcolor='#E0E0FF'> trashes edits to brain.finalsurfs.manedit.mgz ||
||<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.||
||<bgcolor='#FFFFE0'>'''-notal-check'''||<-5(bgcolor='#E0E0FF'>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 ||
||<bgcolor='#FFFFE0'>'''-gcut'''||<-5(bgcolor='#E0E0FF'>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. <<BR>>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. ||
||<bgcolor='#FFFFE0'>'''-surfsegedit'''||<-5(bgcolor='#E0E0FF'>this flag fixes the gm and a few other areas in the aseg using info from the surfaces. Run after the surfaces are done. ||
||<bgcolor='#FFFFE0'>'''-multistrip'''||<-5(bgcolor='#E0E0FF'>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. ||
||<bgcolor='#FFFFE0'>'''-deface'''||<bgcolor='#E0E0FF'>removes the face from the orig volume to anonymize it.||
||<bgcolor='#FFFFE0'>'''-vno_match_check'''||<bgcolor='#E0E0FF'> 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.||

||<rowbgcolor='#80FF80'>'''recon-all flag'''||'''Used with step'''||'''Description'''||
||<|2(bgcolor='#FFFFE0'>'''-no-ca-align'''||<bgcolor='#FFFFE0'>-careg||<|2(bgcolor='#E0E0FF'>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='#E0E0FF'>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'>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'>'''-jacobian_dist0'''||<bgcolor='#FFFFE0'> ||<bgcolor='#E0E0FF'>Computes how much an individual surface must be distorted in order to perfectly match the atlas (ie, distance contraints are turned off). ||
||<|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||


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):

||<rowbgcolor='#80FF80'>'''recon-all step'''||'''Individual Flag'''||'''Input'''||'''Command Line'''||'''Output'''||
||<|30(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||
-Line 23:
+Line 67:
-||<|3(bgcolor='#FFFFE0'>-careg||<bgcolor='#E0E0FF'>brain.mgz||<|3(bgcolor='#E0E0FF'>["mri_ca_register"] -cross-sequence -mask brain.mgz -T transforms/talairach.lta norm.mgz $GCA transforms/talairach.m3z||<|3(bgcolor='#E0E0FF'>transforms/talairach.m3z||
||<rowbgcolor='#E0E0FF'>transforms/talairach.lta||
||<rowbgcolor='#E0E0FF'>norm.mgz||
||<|2(bgcolor='#FFFFE0'>-calabel||<bgcolor='#E0E0FF'>norm.mgz||<|2(bgcolor='#E0E0FF'>["mri_ca_label"] -cross-sequence norm.mgz transforms/talairach.m3z $GCA aseg.mgz||<|2(bgcolor='#E0E0FF'>aseg.mgz||
||<rowbgcolor='#E0E0FF'>transforms/talairach.m3z||
||<bgcolor='#FFFFE0'>-segstats||<bgcolor='#E0E0FF'>aseg.mgz||<bgcolor='#E0E0FF'>["mri_segstats"] --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --in mri/orig.mgz --ctab-default --excludeid 0 --brain-vol-from-seg --brainmask mri/brain.mgz||<bgcolor='#E0E0FF'>stats/aseg.stats||
||<|4(bgcolor='#FFFFE0'>-normalization2||<bgcolor='#E0E0FF'>brain.mgz||<|2(bgcolor='#E0E0FF'>["mri_normalize"] -mask brain.mgz nu.mgz T1.mgz||<|2(bgcolor='#E0E0FF'>T1.mgz||
||<rowbgcolor='#E0E0FF'>nu.mgz||
||<rowbgcolor='#E0E0FF'>T1.mgz||<|2(>["mri_mask"] T1.mgz brain.mgz brain.mgz||<|2(>brain.mgz||
||<rowbgcolor='#E0E0FF'>brain.mgz||
||<bgcolor='#FFFFE0'>-segmentation||<bgcolor='#E0E0FF'>brain.mgz||<bgcolor='#E0E0FF'>["mri_segment"] brain.mgz wm.mgz||<bgcolor='#E0E0FF'>wm.mgz||
||<|2(bgcolor='#FFFFE0'>-edit_wm_with_aseg||<bgcolor='#E0E0FF'>wm.mgz||<|2(bgcolor='#E0E0FF'>["mri_edit_wm_with_aseg"] wm.mgz aseg.mgz wm.mgz||<|2(bgcolor='#E0E0FF'>wm.mgz||
||<rowbgcolor='#E0E0FF'>aseg.mgz||
||<|2(bgcolor='#FFFFE0'>-fill||<bgcolor='#E0E0FF'>wm.mgz||<|2(bgcolor='#E0E0FF'>["mri_fill"] -a ../scripts/ponscc.cut.log -xform transforms/talairach.xfm -segmentation aseg.mgz wm.mgz filled.mgz||<bgcolor='#E0E0FF'>filled.mgz||
||<rowbgcolor='#E0E0FF'>aseg.mgz||../scripts/ponscc.cut.log||
||<|2((bgcolor='#FFFFE0'>-tessellate||<|2(bgcolor='#E0E0FF'>filled.mgz||<bgcolor='#E0E0FF'>["mri_tessellate"] filled.mgz 255 ../surf/lh.orig||<bgcolor='#E0E0FF'>lh.orig||
||<rowbgcolor='#E0E0FF'>["mri_tessellate"] filled.mgz 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'>-f== FreeSurfer Tutorial: Process Flow ==
+||<|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 ||
-Line 51:
+Line 97:
-||<bgcolor='#FFFFE0'>none||<bgcolor='#FFFFE0'>none||<bgcolor='#E0E0FF'>file.dcm||<bgcolor='#E0E0FF'>["mri_convert"] file.dcm orig/001.mgz||<bgcolor='#E0E0FF'>orig/001.mgz||
||<|10(bgcolor='#FFFFE0'>["recon-all"] -autorecon1 -subjid subj||
||<|3(bgcolor='#FFFFE0'>-motioncor||<bgcolor='#E0E0FF'>orig/001.mgz||<|2(bgcolor='#E0E0FF'>["mri_motion_correct2"] -i orig/001.mgz -i orig/002.mgz -o rawavg.mgz||<|2(bgcolor='#E0E0FF'>rawavg.mgz||
||<rowbgcolor='#E0E0FF'>orig/002.mgz||
||<rowbgcolor='#E0E0FF'>rawavg.mgz||["mri_convert"] rawavg.mgz orig.mgz --conform||orig.mgz||
||<|3(bgcolor='#FFFFE0'>-nuintensitycor||<bgcolor='#E0E0FF'>orig.mgz||<bgcolor='#E0E0FF'>["mri_convert"] orig.mgz orig.mnc||<bgcolor='#E0E0FF'>orig.mnc||
||<rowbgcolor='#E0E0FF'>orig.mnc||(4 iterations of) ["nu_correct"] -clobber nu0.mnc nu1.mnc||nu4.mnc||
||<rowbgcolor='#E0E0FF'>nu4.mnc||["mri_convert"] nu4.mnc nu.mgz||nu.mgz||
||<bgcolor='#FFFFE0'>-talairach||<bgcolor='#E0E0FF'>nu.mgz||<bgcolor='#E0E0FF'>["talairach2"] subjid -mgz||<bgcolor='#E0E0FF'>transforms/talairach.xfm||
||<bgcolor='#FFFFE0'>-normalization||<bgcolor='#E0E0FF'>nu.mgz||<bgcolor='#E0E0FF'>["mri_normalize"] nu.mgz T1.mgz||<bgcolor='#E0E0FF'>T1.mgz||
||<bgcolor='#FFFFE0'>-skullstrip||<bgcolor='#E0E0FF'>T1.mgz||<bgcolor='#E0E0FF'>["mri_watershed"] T1.mgz brain.mgz||<bgcolor='#E0E0FF'>brain.mgz||
||<-5(rowbgcolor='#FF8080'>Check skullstrip (brain.mgz), talairach (transforms/talairach.xfm), and normalization (brain.mgz or T1.mgz - mean wm voxel value = 110)||
||<|36(bgcolor='#FFFFE0'>["recon-all"] -autorecon2 -subjid subj||
||<|2(bgcolor='#FFFFE0'>-gcareg||<bgcolor='#E0E0FF'>brain.mgz||<|2(bgcolor='#E0E0FF'>["mri_em_register"] -mask brain.mgz -p .5 -fsamples fsamples.mgz nu.mgz $GCA transforms/talairach.lta||<|2(bgcolor='#E0E0FF'>transforms/talairach.lta||
||<rowbgcolor='#E0E0FF'>nu.mgz||
||<|3(bgcolor='#FFFFE0'>-canorm||<bgcolor='#E0E0FF'>brain.mgz||<|3(bgcolor='#E0E0FF'>["mri_ca_normalize"] -mask brain.mgz nu.mgz $GCA transforms/talairach.lta norm.mgz||<|3(bgcolor='#E0E0FF'>norm.mgz||
||<rowbgcolor='#E0E0FF'>nu.mgz||
||<rowbgcolor='#E0E0FF'>transforms/talairach.lta||
||<|3(bgcolor='#FFFFE0'>-careg||<bgcolor='#E0E0FF'>brain.mgz||<|3(bgcolor='#E0E0FF'>["mri_ca_register"] -cross-sequence -mask brain.mgz -T transforms/talairach.lta norm.mgz $GCA transforms/talairach.m3z||<|3(bgcolor='#E0E0FF'>transforms/talairach.m3z||
||<rowbgcolor='#E0E0FF'>transforms/talairach.lta||
+||<|24(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||
-Line 72:
+Line 100:
-||<|2(bgcolor='#FFFFE0'>-calabel||<bgcolor='#E0E0FF'>norm.mgz||<|2(bgcolor='#E0E0FF'>["mri_ca_label"] -cross-sequence norm.mgz transforms/talairach.m3z $GCA aseg.mgz||<|2(bgcolor='#E0E0FF'>aseg.mgz||
||<rowbgcolor='#E0E0FF'>transforms/talairach.m3z||
||<bgcolor='#FFFFE0'>-segstats||<bgcolor='#E0E0FF'>aseg.mgz||<bgcolor='#E0E0FF'>["mri_segstats"] --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --in mri/orig.mgz --ctab-default --excludeid 0 --brain-vol-from-seg --brainmask mri/brain.mgz||<bgcolor='#E0E0FF'>stats/aseg.stats||
||<|4(bgcolor='#FFFFE0'>-normalization2||<bgcolor='#E0E0FF'>brain.mgz||<|2(bgcolor='#E0E0FF'>["mri_normalize"] -mask brain.mgz nu.mgz T1.mgz||<|2(bgcolor='#E0E0FF'>T1.mgz||
||<rowbgcolor='#E0E0FF'>nu.mgz||
||<rowbgcolor='#E0E0FF'>T1.mgz||<|2(>["mri_mask"] T1.mgz brain.mgz brain.mgz||<|2(>brain.mgz||
||<rowbgcolor='#E0E0FF'>brain.mgz||
||<bgcolor='#FFFFE0'>-segmentation||<bgcolor='#E0E0FF'>brain.mgz||<bgcolor='#E0E0FF'>["mri_segment"] brain.mgz wm.mgz||<bgcolor='#E0E0FF'>wm.mgz||
||<|2(bgcolor='#FFFFE0'>-edit_wm_with_aseg||<bgcolor='#E0E0FF'>wm.mgz||<|2(bgcolor='#E0E0FF'>["mri_edit_wm_with_aseg"] wm.mgz aseg.mgz wm.mgz||<|2(bgcolor='#E0E0FF'>wm.mgz||
-Line 82:
+Line 101:
-||<|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||
+||<|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 96:
+Line 112:
-||<|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||
+||<|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||
-Line 99:
+Line 121:
-||<-5(rowbgcolor='#FF8080'>Check final surfaces '''tkmedit subj wm.mgz ?h.white brain.mgz'''||
||<|8(bgcolor='#FFFFE0'>["recon-all"] -autorecon3 -subjid subj||
||<bgcolor='#FFFFE0'>-sphere||<bgcolor='#E0E0FF'>?h.inflated||<bgcolor='#E0E0FF'>["mris_sphere"] -w 0 ?h.inflated ?h.sphere||<bgcolor='#E0E0FF'>?h.sphere||
||<bgcolor='#FFFFE0'>-surfreg||<bgcolor='#E0E0FF'>?h.sphere||<bgcolor='#E0E0FF'>["mris_register"] -w 0 -curv ?h.sphere $AvgTif ?h.sphere.reg||<bgcolor='#E0E0FF'>?h.sphere.reg||
||<|2(bgcolor='#FFFFE0'>-contrasurfreg||<bgcolor='#E0E0FF'>rh.sphere||<bgcolor='#E0E0FF'>["mris_register"] -w 0 -curv -reverse rh.sphere $AvgTif rh.lh.sphere.reg||<bgcolor='#E0E0FF'>rh.lh.sphere.reg||
||<rowbgcolor='#E0E0FF'>lh.sphere||["mris_register"] -w 0 -curv -reverse lh.sphere $AvgTif lh.rh.sphere.reg||lh.rh.sphere.reg||
||<bgcolor='#FFFFE0'>-avgcurv||<bgcolor='#E0E0FF'>?h.sphere.reg||<bgcolor='#E0E0FF'>["mrisp_paint"] -a 5 $AvgTif#6 ?h.sphere.reg ?h.avg_curv||<bgcolor='#E0E0FF'>?h.avg_curv||
||<bgcolor='#FFFFE0'>-cortparc||<bgcolor='#E0E0FF'>?h.sphere.reg||<bgcolor='#E0E0FF'>["mris_ca_label"] -t $CPAnnotTable subj ?h sphere.reg $CPAtlas ?h.aparc.annot||<bgcolor='#E0E0FF'>label/?h.aparc.annot||
||<bgcolor='#FFFFE0'>-parcstats||<bgcolor='#E0E0FF'>label/?h.aparc.annot||<bgcolor='#E0E0FF'>["mris_anatomical_stats"] -f scripts/?h.aparc.stats -b -a label/?h.aparc.annot subj ?h||<bgcolor='#E0E0FF'>stats/?h.aparc.stats||
inalsurfs||<bgcolor='#E0E0FF'>brain.mgz||<|3(bgcolor='#E0E0FF'>["mris_make_surfaces"] -w 0 subj ?h||<bgcolor='#E0E0FF'>?h.white||
||<|2(rowbgcolor='#E0E0FF'>?h.orig||?h.pial||
+||<rowbgcolor='#80FF80'>'''recon-all step'''||'''Individual Flag'''||'''Input'''||'''Command Line'''||'''Output'''||
||<|13(bgcolor='#FFFFE0'>'''[[recon-all]] -autorecon2-pial -subjid subj '''(use this after editing brain.finalsurfs.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 111:
+Line 128:
-||<|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||
+||<|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||
-Line 114:
+Line 137:
-||<-5(rowbgcolor='#FF8080'>Check final surfaces '''tkmedit subj wm.mgz ?h.white brain.mgz'''||
||<|8(bgcolor='#FFFFE0'>["recon-all"] -autorecon3 -subjid subj||
||<bgcolor='#FFFFE0'>-sphere||<bgcolor='#E0E0FF'>?h.inflated||<bgcolor='#E0E0FF'>["mris_sphere"] -w 0 ?h.inflated ?h.sphere||<bgcolor='#E0E0FF'>?h.sphere||
||<bgcolor='#FFFFE0'>-surfreg||<bgcolor='#E0E0FF'>?h.sphere||<bgcolor='#E0E0FF'>["mris_register"] -w 0 -curv ?h.sphere $AvgTif ?h.sphere.reg||<bgcolor='#E0E0FF'>?h.sphere.reg||
||<|2(bgcolor='#FFFFE0'>-contrasurfreg||<bgcolor='#E0E0FF'>rh.sphere||<bgcolor='#E0E0FF'>["mris_register"] -w 0 -curv -reverse rh.sphere $AvgTif rh.lh.sphere.reg||<bgcolor='#E0E0FF'>rh.lh.sphere.reg||
||<rowbgcolor='#E0E0FF'>lh.sphere||["mris_register"] -w 0 -curv -reverse lh.sphere $AvgTif lh.rh.sphere.reg||lh.rh.sphere.reg||
||<bgcolor='#FFFFE0'>-avgcurv||<bgcolor='#E0E0FF'>?h.sphere.reg||<bgcolor='#E0E0FF'>["mrisp_paint"] -a 5 $AvgTif#6 ?h.sphere.reg ?h.avg_curv||<bgcolor='#E0E0FF'>?h.avg_curv||
||<bgcolor='#FFFFE0'>-cortparc||<bgcolor='#E0E0FF'>?h.sphere.reg||<bgcolor='#E0E0FF'>["mris_ca_label"] -t $CPAnnotTable subj ?h sphere.reg $CPAtlas ?h.aparc.annot||<bgcolor='#E0E0FF'>label/?h.aparc.annot||
||<bgcolor='#FFFFE0'>-parcstats||<bgcolor='#E0E0FF'>label/?h.aparc.annot||<bgcolor='#E0E0FF'>["mris_anatomical_stats"] -f scripts/?h.aparc.stats -b -a label/?h.aparc.annot subj ?h||<bgcolor='#E0E0FF'>stats/?h.aparc.stats||
-Line 124:
+Line 138:
+||<rowbgcolor='#80FF80'>'''recon-all step'''||'''Individual Flag'''||'''Input'''||'''Command Line'''||'''Output'''||
||<|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||
||<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||
||<|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||