Diff for "OtherUsefulFlags" - Free Surfer Wiki

Differences between revisions 1 and 10 (spanning 9 versions)

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
-usecontrolpoints	-normalization	nu.mgz	["mri_normalize"] -f $SUBJECTS_DIR/subjid/tmp/control.dat nu.mgz T1.mgz	T1.mgz	uses control points, saved to tmp/control.dat to modify the normalization
-keepwmedits	-segmentation	brain.mgz	["mri_segment"] -keep brain.mgz wm.mgz	wm.mgz	preserves any previous edits to wm volume
-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
-rerun					this flag will re-run your subject with a new version while maintaining all the manual changes you've made.

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

-  ⇤ ← Revision 1 as of 2005-10-18 11:45:29 → 
  Size: 15095
  Editor: JenniPacheco
  Comment:
+   ← Revision 10 as of 2005-12-05 18:41:20 → ⇥
  Size: 11719
  Editor: JenniPacheco
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 3:
+The following flags can be used in conjunction with individual steps or the entire process:
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+Line 5:
-||<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='#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||
||<|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.||
-Line 20:
+Line 15:
-||<|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||
+||<|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||
-Line 23:
+Line 18:
-||<|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||
+||<|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||
-Line 26:
+Line 21:
-||<|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||
+||<|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||
-Line 28:
+Line 23:
-||<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||
+||<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'>-rerun||<bgcolor='#FFFFE0'>||<bgcolor='#E0E0FF'>||<bgcolor='#E0E0FF'>||<bgcolor='#E0E0FF'>||<bgcolor='#FFFFE0'>this flag will re-run your subject with a new version while maintaining all the manual changes you've made.||

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

||<rowbgcolor='#80FF80'>'''recon-all step'''||'''Individual Flag'''||'''Input'''||'''Command Line'''||'''Output'''||
||<|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||
-Line 33:
+Line 38:
-||<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 ==


||<rowbgcolor='#80FF80'>'''recon-all step'''||'''Individual Flag'''||'''Input'''||'''Command Line'''||'''Output'''||
||<bgcolor='#FFFFE0'>none||<bgcolor='#FFFFE0'>none||<bgcolor='#E0E0FF'>file.dcm||<bgcolor='#E0E0FF'>["mri_convert"] file.dcm orig/001.mgz||<bgcolor='#E0E0FF'>orig/001.mgz||
||<|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||
||<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||
+||<bgcolor='#FFFFE0'>-segmentation||<bgcolor='#E0E0FF'>brain.mgz||<bgcolor='#E0E0FF'>["mri_segment"] -keep brain.mgz wm.mgz||<bgcolor='#E0E0FF'>wm.mgz||
-Line 99:
+Line 58:
-||<-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||
+||<rowbgcolor='#80FF80'>'''recon-all step'''||'''Individual Flag'''||'''Input'''||'''Command Line'''||'''Output'''||
||<|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||
-Line 114:
+Line 79:
-||<-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 80:
+||<rowbgcolor='#80FF80'>'''recon-all step'''||'''Individual Flag'''||'''Input'''||'''Command Line'''||'''Output'''||
||<|7(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||
||<rowbgcolor='#E0E0FF'>?h.thickness||
||<|3(bgcolor='#FFFFE0'>-cortribbon||<bgcolor='#E0E0FF'>orig.mgz||<|3(bgcolor='#E0E0FF'>["mri_surf2vol"] --mkmask --hemi ?h --fillribbon --template orig.mgz --volregidentity subj --outvol ?h.ribbon.mgz||<|3(bgcolor='#E0E0FF'>?h.ribbon.mgz||
||<rowbgcolor='#E0E0FF'>?h.white||
||<rowbgcolor='#E0E0FF'>?h.pial||