FreeSurfer Tutorial: Process Flow
This table shows the recon-all steps for the current dev version of FreeSurfer (available here). It does not document the stable, publicly released, version of Freesurfer (v6.0). See ReconAllTableStableV6.0 to see a process flow for the latest stable version of FreeSurfer.
See also the OtherUsefulFlags for other recon-all options.
recon-all step |
Individual Flag |
Input |
Command Line |
Output |
recon-all -autorecon1 -subjid <subjid> |
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-i <invol1> |
invol1.dcm or .nii or .mgz |
mri_convert invol1.dcm orig/001.mgz |
orig/001.mgz |
|
-i <invol2> optional |
invol2.dcm or .nii or .mgz |
mri_convert invol2.dcm orig/002.mgz |
orig/002.mgz |
|
-T2 <invol> or |
invol.dcm or .nii or .mgz |
mri_convert --no_scale 1 invol.dcm orig/T2raw.mgz |
orig/T2raw.mgz |
|
orig/001.mgz |
mri_robust_template --mov 001.mgz 002.mgz --average 1 --template rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout --subsample 200 --lta |
rawavg.mgz |
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orig/002.mgz |
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rawavg.mgz |
mri_convert rawavg.mgz orig.mgz --conform |
orig.mgz |
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orig.mgz |
mri_add_xform_to_header -c transforms/talairach.xfm orig.mgz orig.mgz |
orig.mgz |
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orig.mgz |
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz |
orig_nu.mgz |
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orig_nu.mgz |
talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm |
transforms/talairach.auto.xfm |
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transforms/talairach.auto.xfm |
cp transforms/talairach.auto.xfm transforms/talairach.xfm |
transforms/talairach.xfm |
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transforms/talairach.xfm |
talairach_afd -T 0.005 -xfm transforms/talairach.xfm |
|
||
|
awk -f $FREESURFER_HOME/bin/extract_talairach_avi_QA.awk transforms/talairach_avi.log |
transforms/talairach_avi.log |
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orig.mgz |
mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 |
nu.mgz |
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talairach.xfm |
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nu.mgz |
mri_normalize -g 1 -mprage nu.mgz T1.mgz |
T1.mgz |
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nu.mgz |
mri_em_register -skull nu.mgz $FREESURFER_HOME/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta |
transforms/talairach_with_skull.lta |
||
T1.mgz |
mri_watershed -T1 -brain_atlas $FREESURFER_HOME/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz |
brainmask.auto.mgz |
||
brainmask.auto.mgz |
cp brainmask.auto.mgz brainmask.mgz |
brainmask.mgz |
recon-all step |
Individual Flag |
Input |
Command Line |
Output |
recon-all -autorecon2 -subjid <subjid> |
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brainmask.mgz |
mri_em_register -uns 3 -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta |
transforms/talairach.lta |
||
nu.mgz |
||||
brainmask.mgz |
mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta norm.mgz |
norm.mgz |
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nu.mgz |
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transforms/talairach.lta |
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brainmask.mgz |
mri_ca_register -align-after -nobigventricles -mask brainmask.mgz -T transforms/talairach.lta norm.mgz $FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca transforms/talairach.m3z |
transforms/talairach.m3z |
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transforms/talairach.lta |
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norm.mgz |
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norm.mgz |
mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz |
aseg.auto_noCCseg.mgz |
||
transforms/talairach.m3z |
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aseg.auto_noCCseg.mgz |
mri_cc -lta <subjid>/mri/transforms/cc_up.lta -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz <subjid> |
aseg.auto.mgz |
||
aseg.auto.mgz |
cp aseg.auto.mgz aseg.presurf.mgz |
aseg.presurf.mgz |
||
brainmask.mgz |
mri_normalize -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz |
brain.mgz |
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norm.mgz |
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aseg.presurf.mgz |
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brain.mgz |
mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz |
brain.finalsurfs.mgz |
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brainmask.mgz |
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brain.mgz |
mri_segment -mprage 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.presurf.mgz wm.asegedit.mgz |
wm.asegedit.mgz |
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aseg.presurf.mgz |
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brain.mgz |
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wm.asegedit.mgz |
mri_pretess wm.asegedit.mgz wm 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.auto_noCCseg.mgz wm.mgz filled.mgz |
filled.mgz |
|
aseg.auto_noCCseg.mgz |
../scripts/ponscc.cut.log |
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transforms/talairach.lta |
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filled.mgz |
mri_pretess filled.mgz 255 norm.mgz filled-pretess255.mgz |
filled-pretess255.mgz |
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norm.mgz |
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filled-pretess255.mgz |
mri_tessellate filled-pretess255.mgz 255 lh.orig.nofix |
lh.orig.nofix |
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filled.mgz |
mri_pretess filled.mgz 127 norm.mgz filled-pretess127.mgz |
filled-pretess127.mgz |
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norm.mgz |
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filled-pretess127.mgz |
mri_tessellate filled-pretess127.mgz 127 rh.orig.nofix |
rh.orig.nofix |
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?h.orig.nofix |
mris_extract_main_component ?h.orig.nofix ?h.orig.nofix |
?h.orig.nofix |
||
|
rm -f filled-pretess255.mgz filled-pretess127.mgz |
|
||
?h.orig.nofix |
mris_smooth -nw ?h.orig.nofix ?h.smoothwm.nofix |
?h.smoothwm.nofix |
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?h.smoothwm.nofix |
mris_inflate -no-save-sulc ?h.smoothwm.nofix ?h.inflated.nofix |
?h.inflated.nofix |
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?h.inflated.nofix |
mris_sphere -q ?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 |
|
?h.inflated.nofix |
cp ?h.inflated.nofix ?h.inflated |
?h.inflated |
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?h.qsphere.nofix |
mris_fix_topology -mgz -sphere qsphere.nofix -ga <subjid> ?h |
?h.orig |
||
?h.orig |
mris_euler_number ?h.orig |
?h.orig |
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?h.orig |
mris_remove_intersection ?h.orig ?h.orig |
?h.orig |
||
|
rm ?h.inflated |
|
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-white |
aseg.presurf.mgz |
mris_make_surfaces -aseg ../mri/aseg.presurf -whiteonly -noaparc -mgz -T1 brain.finalsurfs <subjid> ?h |
?h.white |
|
brain.finalsurfs.mgz |
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wm.mgz |
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filled.mgz |
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?h.orig |
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?h.curv |
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?h.area |
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?h.cortex.label |
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?h.white |
mris_smooth -n 3 -nw ?h.white ?h.smoothwm |
?h.smoothwm |
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?h.smoothwm |
mris_inflate ?h.smoothwm ?h.inflated |
?h.inflated |
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?h.sulc |
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-curvHK |
?h.white |
mris_curvature -w ?h.white |
?h.white.H |
|
?h.white.K |
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?h.inflated |
mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ?h.inflated |
?h.inflated.H |
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?h.inflated.K |
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-curvstats |
?h.smoothwm |
mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/?h.curv.stats -F smoothwm <subjid> ?h curv sulc |
stats/?h.curv.stats |
|
?h.curv |
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?h.sulc |
recon-all step |
Individual Flag |
Input |
Command Line |
Output |
recon-all -autorecon3 -subjid <subjid> |
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?h.inflated |
mris_sphere ?h.inflated ?h.sphere |
?h.sphere |
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?h.smoothwm |
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?h.sphere |
mris_register -curv ?h.sphere $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif ?h.sphere.reg |
?h.sphere.reg |
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?h.white |
mris_jacobian ?h.white ?h.sphere.reg ?h.jacobian_white |
?h.jacobian_white |
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?h.sphere.reg |
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?h.sphere.reg |
mrisp_paint -a 5 $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif#6 ?h.sphere.reg ?h.avg_curv |
?h.avg_curv |
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aseg.presurf.mgz |
mris_ca_label -l ../label/lh.cortex.label -aseg mri/aseg.presurf.mgz <subjid> ?h ?h.sphere.reg $FREESURFER_HOME/average/?h.curvature.buckner40.filled.desikan_killiany.2007-06-20gcs ?h.aparc.annot |
label/?h.aparc.annot |
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?h.cortex.label |
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?h.sphere.reg |
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-pial |
aseg.presurf.mgz |
mris_make_surfaces -orig_white white -orig_pial white -aseg ../mri/aseg.presurf -nowhite -mgz -T1 brain.finalsurfs <subjid> ?h |
?h.pial |
|
brain.finalsurfs.mgz |
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wm.mgz |
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filled.mgz |
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?h.orig |
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?h.curv.pial |
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?h.area.pial |
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label/?h.aparc.annot |
?h.thickness |
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-T2pial or |
orig/T2raw.mgz |
bbregister --s <subjid> --mov mri/orig/T2raw.mgz --lta mri/transforms/T2raw.lta --init-fsl --T2 |
transforms/T2raw.lta |
|
orig/T2raw.mgz |
mri_convert -odt short -at mri/transforms/T2raw.lta -rt cubic -ns 1 -rl mri/orig.mgz mri/orig/T2raw.mgz mri/T2.prenorm.mgz |
T2.prenorm.mgz |
||
transforms/T2raw.lta |
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aseg.presurf.mgz |
mri_normalize -sigma 0.5 -nonmax_suppress 0 -min_dist 1 -aseg mri/aseg.presurf.mgz -surface surf/rh.white identity.nofile -surface surf/lh.white identity.nofile mri/T2.prenorm.mgz mri/T2.mgz |
T2.mgz |
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?h.white |
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T2.prenorm.mgz |
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?h.pial |
cp -v surf/?h.pial surf/?h.woT2.pial |
?h.woT2.pial |
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aseg.presurf.mgz |
mris_make_surfaces -orig_white white -orig_pial woT2.pial -aseg ../mri/aseg.presurf -nowhite -mgz -T1 brain.finalsurfs -T2 ../mri/T2 -nsigma_above 2 -nsigma_below 5 <subjid> ?h |
?h.pial |
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brain.finalsurfs.mgz |
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wm.mgz |
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filled.mgz |
?h.curv.pial |
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?h.white |
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label/?h.aparc.annot |
?h.area.pial |
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T2.mgz |
?h.thickness |
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?h.woT2.pial |
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aseg.presurf.mgz |
mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon <subjid> |
?h.ribbon.mgz |
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?h.white |
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?h.pial |
ribbon.mgz |
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label/?h.aparc.annot |
mris_anatomical_stats -th3 -mgz -cortex ../label/?h.cortex.label -f stats/?h.aparc.stats -b -a label/?h.aparc.annot -c label/aparc.annot.ctab <subjid> ?h |
stats/?h.aparc.stats |
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wm.mgz, ribbon.mgz |
label/aparc.annot.ctab |
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?h.white |
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?h.pial |
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?h.thickness |
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aseg.presurf.mgz |
mris_ca_label -l ../label/lh.cortex.label -aseg aseg.presurf.mgz <subjid> ?h ?h.sphere.reg $FREESURFER_HOME/average/?h.destrieux.simple.2009-07-29.gcs label/?h.aparc.a2009s.annot |
label/?h.aparc.a2009s.annot |
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?h.sphere.reg |
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label/?h.cortex.label |
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label/?h.aparc.a2009s.annot |
mris_anatomical_stats -th3 -mgz -cortex ../label/?h.cortex.label -f stats/?h.aparc.a2009s.stats -b -a label/?h.aparc.a2009s.annot -c label/aparc.annot.a2009s.ctab <subjid> ?h |
stats/?h.aparc.a2009s.stats |
||
wm.mgz, ribbon.mgz |
label/aparc.annot.a2009s.ctab |
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?h.white |
||||
?h.pial |
||||
?h.thickness |
||||
aseg.presurf.mgz |
mris_ca_label ../label/lh.cortex.label -aseg aseg.presurf.mgz <subjid> ?h ?h.sphere.reg $FREESURFER_HOME/average/?h.DKTatlas.2016-03-20.gcs ../label/?h.aparc.DKTatlas.annot |
label/?h.aparc.DKTatlas.annot |
||
?h.sphere.reg |
||||
label/?h.cortex.label |
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label/?h.aparc.DKTatlas.annot |
mris_anatomical_stats -th3 -mgz -cortex ../label/?h.cortex.label -f stats/?h.aparc.DKTatlas.stats -b -a label/?h.aparc.DKTatlas.annot -c label/aparc.annot.DKTatlas.ctab <subjid> ?h |
stats/?h.aparc.DKTatlas.stats |
||
wm.mgz, ribbon.mgz |
label/aparc.annot.DKTatlas.ctab |
|||
?h.white |
||||
?h.pial |
||||
?h.thickness |
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-pctsurfcon |
rawavg.mgz |
pctsurfcon --s <subjid> --?h-only |
?h.w-g.pct.mgh |
|
orig.mgz |
||||
?h.cortex.label |
stats/?h.w-g.pct.stats |
|||
?h.white |
||||
-hyporelabel |
aseg.presurf.mgz |
mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz |
aseg.presurf.hypos.mgz |
|
?h.white |
||||
aseg.presurf.hypos.mgz |
mri_aparc2aseg --s <subjid> --ribbon |
aparc+aseg.mgz |
||
?h.ribbon.mgz |
||||
label/?h.aparc.annot |
||||
ribbon.mgz |
||||
aseg.presurf.hypos.mgz |
mri_aparc2aseg --s <subjid> --ribbon --annot aparc.a2009s |
aparc.a2009s+aseg.mgz |
||
?h.ribbon.mgz |
||||
label/?h.aparc.a2009s.annot |
||||
ribbon.mgz |
||||
aseg.presurf.hypos.mgz |
mri_aparc2aseg --s <subjid> --ribbon --annot aparc.DKTatlas |
aparc.DKTatlas+aseg.mgz |
||
?h.ribbon.mgz |
||||
label/?h.aparc.DKTatlas.annot |
||||
ribbon.mgz |
||||
-apas2aseg |
aparc+aseg.mgz |
apas2aseg --i aparc+aseg.mgz --o aseg.mgz |
aseg.mgz |
|
brainmask.mgz, norm.mgz, aseg.mgz, aseg.presurf.mgz, ribbon.mgz |
mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --totalgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab $FREESURFER_HOME/ASegStatsLUT.txt --subject <subjid> |
stats/aseg.stats |
||
?h.orig.nofix, ?h.white, ?h.pial |
||||
aparc+aseg.mgz |
mri_aparc2aseg --s <subjid> --labelwm --hypo-as-wm --rip-unknown --ribbon --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz |
wmparc.mgz |
||
talairach.xfm, brainmask.mgz, norm.mgz, ribbon.mgz, wmparc.mgz, aseg.presurf.mgz, ?h.white, ?h.pial |
mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject <subjid> --surf-wm-vol --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt |
stats/wmparc.stats |
||
?h.sphere.reg |
mri_label2label --srcsubject fsaverage --srclabel fsaverage/label/?h.BA*.label --trgsubject <subjid> --trglabel ?h.BA*.label --hemi ?h --regmethod surface |
label/?h.BA*_exvivo.label label/?h.perirhinal_exvivo.label label/?h.entorhinal_exvivo.label |