FreeSurfer Tutorial: Process Flow
This table shows the recon-all steps for stable version 5.1 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> -i <invol2> |
invol1.dcm |
mri_convert invol1.dcm orig/001.mgz |
orig/001.mgz |
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invol2.dcm |
mri_convert invol2.dcm orig/002.mgz |
orig/002.mgz |
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orig/001.mgz |
mri_robust_template --mov 001.mgz 002.mgz --average 1 --template rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --subsample 200 |
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 |
talairach_avi --i orig.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 |
transforms/talairach.xfm |
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awk -f $FREESURFER_HOME/bin/extract_talairach_avi_QA.awk transforms/talairach_avi.log |
transforms/talairach_avi.log |
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orig.mgz, talairach.xfm |
mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 --uchar transforms/talairach.xfm |
nu.mgz |
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nu.mgz |
mri_normalize -g 1 nu.mgz T1.mgz |
T1.mgz |
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nu.mgz |
mri_em_register -skull nu.mgz $FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta |
transforms/talairach_with_skull.lta |
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T1.mgz |
mri_watershed -T1 -brain_atlas $FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz |
brainmask.auto.mgz |
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brainmask.auto.mgz |
cp brainmask.auto.mgz brainmask.mgz |
brainmask.mgz |
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recon-all -autorecon2 -subjid <subjid> |
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brainmask.mgz |
mri_em_register -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB_all_2008-03-26.gca transforms/talairach.lta |
transforms/talairach.lta |
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nu.mgz |
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brainmask.mgz |
mri_ca_normalize -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB_all_2008-03-26.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_2008-03-26.gca transforms/talairach.m3z |
transforms/talairach.m3z |
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transforms/talairach.lta |
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norm.mgz |
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transforms/talairach.m3z |
mri_ca_register -invert-and-save transforms/talairach.m3z |
transforms/talairach.m3z.inv.x.mgz |
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transforms/talairach.m3z.inv.y.mgz |
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transforms/talairach.m3z.inv.z.mgz |
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nu.mgz |
mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2008-03-26.gca nu_noneck.mgz |
nu_noneck.mgz |
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transforms/talairach.m3z |
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transforms/talairach.lta |
mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz $FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta |
transforms/talairach_with_skull.lta |
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nu_noneck.mgz |
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norm.mgz |
mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz |
aseg.auto_noCCseg.mgz |
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transforms/talairach.m3z |
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aseg.auto_noCCseg.mgz |
mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz <subjid> |
aseg.auto.mgz |
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aseg.auto.mgz |
cp aseg.auto.mgz aseg.mgz |
aseg.mgz |
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brainmask.mgz |
mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz |
brain.mgz |
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norm.mgz |
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aseg.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 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 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 |
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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 |
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rm -f filled-pretess255.mgz filled-pretess127.mgz |
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?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 |
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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 -mgz -sphere qsphere.nofix -ga <subjid> ?h |
?h.orig |
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?h.orig |
mris_euler_number ?h.orig |
?h.orig |
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?h.orig |
mris_remove_intersection ?h.orig ?h.orig |
?h.orig |
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rm ?h.inflated |
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-white |
aseg.mgz, brain.finalsurfs.mgz, wm.mgz, filled.mgz |
mris_make_surfaces -whiteonly -noaparc -mgz -T1 brain.finalsurfs <subjid> ?h |
?h.white |
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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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?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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recon-all -autorecon3 -subjid <subjid> |
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?h.inflated,?h.smoothwm |
mris_sphere ?h.inflated ?h.sphere |
?h.sphere |
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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.mgz, ?h.cortex.label |
mris_ca_label -l ../label/lh.cortex.label -aseg mri/aseg.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.sphere.reg |
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-pial |
aseg.mgz, brain.finalsurfs.mgz, wm.mgz, filled.mgz |
mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs <subjid> ?h |
?h.pial |
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?h.orig, label/?h.aparc.annot |
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?h.curv.pial, ?h.area.pial |
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?h.thickness |
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?h.area |
mris_calc -o ?h.area.mid ?h.area add ?h.area.pial |
?h.area.mid |
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?h.area.pial |
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?h.area.mid |
mris_calc -o ?h.area.mid ?h.area.mid div 2 |
?h.area.mid |
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?h.area.mid |
mris_calc -o ?h.volume ?h.area.mid mul ?h.thickness |
?h.volume |
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?h.thickness |
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label/?h.aparc.annot |
mris_anatomical_stats -mgz -f stats/?h.aparc.stats -b -a label/?h.aparc.annot -c label/aparc.annot.ctab <subjid> ?h |
stats/?h.aparc.stats label/aparc.annot.ctab |
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aseg.mgz, ?h.cortex.label |
mris_ca_label -l ../label/lh.cortex.label -aseg aseg.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.aparc.a2009s.annot |
mris_anatomical_stats -mgz -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 stats/aparc.annot.a2009s.ctab |
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aseg.mgz |
mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance <subjid> |
?h.ribbon.mgz, ribbon.mgz |
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?h.white |
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?h.pial |
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aseg.mgz |
mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --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 --ctab $FREESURFER_HOME/ASegStatsLUT.txt --subject <subjid> |
stats/aseg.stats |
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aseg.mgz |
mri_aparc2aseg --s <subjid> --ribbon |
aparc+aseg.mgz |
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?h.ribbon.mgz |
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label/?h.aparc.annot |
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aseg.mgz |
mri_aparc2aseg --s <subjid> --ribbon --a2009s |
aparc.a2009s+aseg.mgz |
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?h.ribbon.mgz |
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label/?h.aparc.a2009s.annot |
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aparc+aseg.mgz |
mri_aparc2aseg --s <subjid> --labelwm --hypo-as-wm --rip-unknown --ribbon --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz |
wmparc.mgz |
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wmparc.mgz |
mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --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 |
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?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*.label |
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-label-exvivo-ec |
?h.sphere.reg |
mris_spherical_average -erode 1 -orig white -t 0.4 -o <subjid> label ?h.entorhinal ?h sphere.reg ?h.EC_average ?h.entorhinal_exvivo.label |
label/?h.entorhinal_exvivo.label |
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