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||<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'>'''-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). || |
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. |
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-all |
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-dontrun |
useful for debugging. just prints the commands that will run (does not execute them). |
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-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 |
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-clean-seed |
trashes all saved seed point for the cutting planes and uses the automatically set cutting planes. |
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-clean-cp |
trashes control points and runs the normalization without control points. |
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-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 |
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-clean-wm |
trashes any manual edits to the wm.mgz volume and runs using the automatically generated wm.mgz. |
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-clean-aseg |
trashes any manual edits to the aseg.mgz and runs using the automatically generated aseg.mgz |
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-clean-cpwm |
combination of -clean-cp and -clean-wm. |
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-clean |
use this flag to clear all of your manual edits and run it completely fresh. |
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-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. |
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-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. |
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-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. |
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. |
-calabel |
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-subcortseg |
-gcareg |
runs the subcortical segmentation and associated statistics |
-canorm |
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-careg |
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-rmneck |
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-skull-lta |
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-calabel |
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-segstats |
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-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 |
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Computes how much an individual surface must be distorted in order to perfectly match the atlas (ie, distance contraints are turned off). |
-old-atlas |
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-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. |
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-canorm |
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-careg |
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-calabel |
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-surfreg |
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-contrasurfreg |
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-avgcurv |
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-cortparc |
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-deface |
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) |
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-normalization2 |
brainmask.mgz |
mri_normalize -mask brainmask.mgz norm.mgz brain.mgz |
brain.mgz |
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norm.mgz |
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brain.mgz |
mri_mask brain.mgz brainmask.mgz brain.finalsurfs.mgz |
brain.finalsurfs.mgz |
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brainmask.mgz |
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-segmentation |
brain.mgz |
mri_segment brain.mgz wm.seg.mgz |
wm.seg.mgz |
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wm.seg.mgz |
mri_edit_wm_with_aseg wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz |
wm.asegedit.mgz |
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aseg.mgz |
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brain.mgz |
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wm.asegedit.mgz |
mri_pretess wm.asegedit.mgz norm.mgz wm.mgz |
wm.mgz |
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norm.mgz |
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-fill |
wm.mgz |
mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.mgz wm.mgz filled.mgz |
filled.mgz |
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aseg.mgz |
../scripts/ponscc.cut.log |
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transforms/talairach.lta |
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-tessellate |
filled.mgz |
mri_tessellate filled.mgz 255 ../surf/lh.orig.nofix |
lh.orig.nofix |
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mri_tessellate filled.mgz 127 ../surf/rh.orig.nofix |
rh.orig.nofix |
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-smooth1 |
?h.orig.nofix |
mris_smooth -nw ?h.orig.nofix ?h.smoothwm.nofix |
?h.smoothwm.nofix |
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-inflate1 |
?h.smoothwm.nofix |
mris_inflate -no-save-sulc ?h.smoothwm.nofix ?h.inflated.nofix |
?h.inflated.nofix |
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-qsphere |
?h.inflated.nofix |
mris_sphere -q -0 ?h.inflated.nofix ?h.inflated.nofix ?h.qsphere.nofix |
?h.qsphere.nofix |
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-fix |
?h.orig.nofix |
cp ?h.orig.nofix ?h.orig |
?h.orig |
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?h.inflated.nofix |
cp ?h.inflated.nofix ?h.inflated |
?h.inflated |
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?h.qsphere.nofix |
mris_fix_topology -errors -mgz -sphere qsphere.nofix -ga <subjid> ?h |
?h.orig |
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-finalsurfs |
brain.finalsurfs.mgz |
mris_make_surfaces -mgz -w 0 -T1 brain.finalsurfs.mgz subj ?h |
?h.white |
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?h.pial |
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?h.thickness |
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?h.orig |
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?h.curv |
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?h.area |
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-smooth2 |
?h.white |
mris_smooth ?h.white ?h.smoothwm |
?h.smoothwm |
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-inflate2 |
?h.white |
mris_inflate ?h.white ?h.inflated |
?h.inflated |
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?h.sulc |
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-cortribbon |
orig.mgz |
mri_surf2vol --mkmask --hemi ?h --fillribbon --template orig.mgz --volregidentity subj --outvol ?h.ribbon.mgz |
?h.ribbon.mgz |
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?h.white |
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?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) |
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-fill |
wm.mgz |
mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.mgz wm.mgz filled.mgz |
filled.mgz |
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aseg.mgz |
../scripts/ponscc.cut.log |
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transforms/talairach.lta |
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-tessellate |
filled.mgz |
mri_tessellate filled.mgz 255 ../surf/lh.orig.nofix |
lh.orig.nofix |
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mri_tessellate filled.mgz 127 ../surf/rh.orig.nofix |
rh.orig.nofix |
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-smooth1 |
?h.orig.nofix |
mris_smooth -nw ?h.orig.nofix ?h.smoothwm.nofix |
?h.smoothwm.nofix |
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-inflate1 |
?h.smoothwm.nofix |
mris_inflate -no-save-sulc ?h.smoothwm.nofix ?h.inflated.nofix |
?h.inflated.nofix |
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-qsphere |
?h.inflated.nofix |
mris_sphere -q -0 ?h.inflated.nofix ?h.inflated.nofix ?h.qsphere.nofix |
?h.qsphere.nofix |
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-fix |
?h.orig.nofix |
cp ?h.orig.nofix ?h.orig |
?h.orig |
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?h.inflated.nofix |
cp ?h.inflated.nofix ?h.inflated |
?h.inflated |
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?h.qsphere.nofix |
mris_fix_topology -errors -mgz -sphere qsphere.nofix -ga <subjid> ?h |
?h.orig |
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-finalsurfs |
brain.finalsurfs.mgz |
mris_make_surfaces -mgz -w 0 -T1 brain.finalsurfs.mgz subj ?h |
?h.white |
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?h.pial |
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?h.thickness |
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?h.orig |
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?h.curv |
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?h.area |
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-smooth2 |
?h.white |
mris_smooth ?h.white ?h.smoothwm |
?h.smoothwm |
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-inflate2 |
?h.white |
mris_inflate ?h.white ?h.inflated |
?h.inflated |
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?h.sulc |
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-cortribbon |
orig.mgz |
mri_surf2vol --mkmask --hemi ?h --fillribbon --template orig.mgz --volregidentity subj --outvol ?h.ribbon.mgz |
?h.ribbon.mgz |
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?h.white |
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?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) |
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-finalsurfs |
brain.finalsurfs.mgz |
mris_make_surfaces -mgz -w 0 -T1 brain.finalsurfs.mgz subj ?h |
?h.white |
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?h.pial |
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?h.thickness |
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?h.orig |
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?h.curv |
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?h.area |
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-smooth2 |
?h.white |
mris_smooth ?h.white ?h.smoothwm |
?h.smoothwm |
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-inflate2 |
?h.white |
mris_inflate ?h.white ?h.inflated |
?h.inflated |
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?h.sulc |
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-cortribbon |
orig.mgz |
mri_surf2vol --mkmask --hemi ?h --fillribbon --template orig.mgz --volregidentity subj --outvol ?h.ribbon.mgz |
?h.ribbon.mgz |
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?h.white |
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?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) |
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-tessellate |
filled.mgz |
mri_tessellate filled.mgz 255 ../surf/lh.orig.nofix |
lh.orig.nofix |
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mri_tessellate filled.mgz 127 ../surf/rh.orig.nofix |
rh.orig.nofix |
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-smooth1 |
?h.orig.nofix |
mris_smooth -nw ?h.orig.nofix ?h.smoothwm.nofix |
?h.smoothwm.nofix |
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-inflate1 |
?h.smoothwm.nofix |
mris_inflate -no-save-sulc ?h.smoothwm.nofix ?h.inflated.nofix |
?h.inflated.nofix |
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-qsphere |
?h.inflated.nofix |
mris_sphere -q -0 ?h.inflated.nofix ?h.inflated.nofix ?h.qsphere.nofix |
?h.qsphere.nofix |
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-fix |
?h.orig.nofix |
cp ?h.orig.nofix ?h.orig |
?h.orig |
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?h.inflated.nofix |
cp ?h.inflated.nofix ?h.inflated |
?h.inflated |
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?h.qsphere.nofix |
mris_fix_topology -errors -mgz -sphere qsphere.nofix -ga <subjid> ?h |
?h.orig |
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-finalsurfs |
brain.finalsurfs.mgz |
mris_make_surfaces -mgz -w 0 -T1 brain.finalsurfs.mgz subj ?h |
?h.white |
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?h.pial |
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?h.thickness |
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?h.orig |
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?h.curv |
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?h.area |
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-smooth2 |
?h.white |
mris_smooth ?h.white ?h.smoothwm |
?h.smoothwm |
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-inflate2 |
?h.white |
mris_inflate ?h.white ?h.inflated |
?h.inflated |
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?h.sulc |
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-cortribbon |
orig.mgz |
mri_surf2vol --mkmask --hemi ?h --fillribbon --template orig.mgz --volregidentity subj --outvol ?h.ribbon.mgz |
?h.ribbon.mgz |
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?h.white |
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?h.pial |