FreeSurfer Tutorial: Process Flow
This table shows the recon-all steps for the latest stable version of FreeSurfer, v4.0.2. See ReconAllDevTable for the dev version of FreeSurfer.
Click here to see this information presented in a block diagram format and here for a process v. files table.
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 |
|
invol2.dcm |
mri_convert invol2.dcm orig/002.mgz |
orig/002.mgz |
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-motioncor |
orig/001.mgz |
mri_motion_correct.fsl -o rawavg.mgz -wild orig/001.mgz orig/002.mgz |
rawavg.mgz |
|
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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-nuintensitycor |
orig.mgz |
mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 |
nu.mgz |
|
-talairach |
nu.mgz |
talairach_avi --i nu.mgz --xfm transforms/talairach.auto.xfm |
transforms/talairach.auto.xfm |
|
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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-normalization |
nu.mgz |
mri_normalize -g 1 nu.mgz T1.mgz |
T1.mgz |
|
-skullstrip |
nu.mgz |
mri_em_register -skull nu.mgz $FREESURFER_HOME/average/RB_all_withskull_2007-08-08.gca transforms/talairach_with_skull.lta |
transforms/talairach_with_skull.lta |
|
T1.mgz |
mri_watershed -T1 -brain_atlas $FREESURFER_HOME/average/RB_all_withskull_2007-08-08.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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-gcareg |
brainmask.mgz |
mri_em_register -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB_all_2007-08-08.gca transforms/talairach.lta |
transforms/talairach.lta |
|
nu.mgz |
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-canorm |
brainmask.mgz |
mri_ca_normalize -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB_all_2007-08-08.gca transforms/talairach.lta norm.mgz |
norm.mgz |
|
nu.mgz |
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transforms/talairach.lta |
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-careg |
brainmask.mgz |
mri_ca_register -align-after -nobigventricles -mask brainmask.mgz -T transforms/talairach.lta norm.mgz $FREESURFER_HOME/average/RB_all_2007-08-08.gca transforms/talairach.m3z |
transforms/talairach.m3z |
|
transforms/talairach.lta |
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norm.mgz |
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-careginv |
transforms/talairach.m3z |
mri_ca_register -invert-and-save transforms/talairach.m3z |
transforms/talairach.m3z.inv.x.mgz |
|
transforms/talairach.m3z.inv.y.mgz |
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transforms/talairach.m3z.inv.z.mgz |
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-rmneck |
nu.mgz |
mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2007-08-08.gca nu_noneck.mgz |
nu_noneck.mgz |
|
transforms/talairach.m3z |
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-skull-lta |
transforms/talairach.lta |
mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz $FREESURFER_HOME/average/RB_all_withskull_2007-08-08.gca transforms/talairach_with_skull.lta |
transforms/talairach_with_skull.lta |
|
nu_noneck.mgz |
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-calabel |
norm.mgz |
mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2007-08-08.gca aseg.auto.mgz |
aseg.auto.mgz |
|
transforms/talairach.m3z |
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aseg.auto.mgz |
cp aseg.auto.mgz aseg.mgz |
aseg.mgz |
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-ccseg |
aseg.mgz |
mri_cc -aseg aseg.auto.mgz -o aseg.auto_CCseg.mgz <subjid> |
aseg.auto_CCseg.mgz |
|
aseg.auto_CCseg.mgz |
cp aseg.auto_CCseg.mgz aseg.mgz |
aseg.mgz |
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-normalization2 |
brainmask.mgz |
mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz |
brain.mgz |
|
norm.mgz |
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aseg.mgz |
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-maskbfs |
brain.mgz |
mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz |
brain.finalsurfs.mgz |
|
brainmask.mgz |
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-segmentation |
brain.mgz |
mri_segment brain.mgz wm.seg.mgz |
wm.seg.mgz |
|
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.mgz wm.mgz filled.mgz |
filled.mgz |
|
aseg.mgz |
../scripts/ponscc.cut.log |
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transforms/talairach.lta |
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-tessellate |
filled.mgz |
mri_pretess filled.mgz 255 norm.mgz filled-pretess255.mgz |
filled-pretess255.mgz |
|
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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-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 ?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 |
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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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-finalsurfs |
brain.finalsurfs.mgz |
mris_make_surfaces -noaparc -mgz -T1 brain.finalsurfs <subjid> ?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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?h.cortex.label |
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-surfvolume |
?h.area |
mris_calc -o ?h.area.mid ?h.area add ?h.area.pial |
?h.area.mid |
|
?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 lh.thickness |
?h.volume |
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?h.volume |
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-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 |
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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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-segstats |
aseg.mgz |
mri_segstats --seg mri/aseg.mgz --sum stats/aseg.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 --surf-wm-vol --ctab $FREESURFER_HOME/ASegStatsLUT.txt --subject <subjid> |
stats/aseg.stats |
|
-cortribbon |
orig.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 |
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?h.white |
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?h.pial |
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recon-all -autorecon3 -subjid <subjid> |
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-sphere |
?h.inflated |
mris_sphere ?h.inflated ?h.sphere |
?h.sphere |
|
-surfreg |
?h.sphere |
mris_register -curv ?h.sphere $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif ?h.sphere.reg |
?h.sphere.reg |
|
-jacobian_white |
?h.white |
mris_jacobian ?h.white ?h.sphere.reg ?h.jacobian_white |
?h.jacobian_white |
|
?h.sphere.reg |
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-avgcurv |
?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 |
|
-cortparc |
aseg.mgz |
mris_ca_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 |
|
?h.sphere.reg |
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-parcstats |
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 |
|
-cortparc2 |
aseg.mgz |
mris_ca_label -aseg aseg.mgz <subjid> ?h ?h.sphere.reg $FREESURFER_HOME/average/?h.atlas2005_simple.gcs label/?h.aparc.a2005s.annot |
label/?h.aparc.a2005s.annot |
|
?h.sphere.reg |
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-parcstats2 |
label/?h.aparc.a2005s.annot |
mris_anatomical_stats -mgz -f stats/?h.aparc.a2005s.stats -b -a label/?h.aparc.a2005s.annot -c label/aparc.annot.a2005s.ctab <subjid> ?h |
stats/?h.aparc.a2005s.stats stats/aparc.annot.a2005s.ctab |
|
-aparc2aseg |
aseg.mgz |
mri_aparc2aseg --s <subjid> --ribbon |
aparc+aseg.mgz |
|
?h.ribbon.mgz |
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label/?h.aparc.annot |
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aseg.mgz |
mri_aparc2aseg --s <subjid> --ribbon --a2005s |
aparc.a2005s+aseg.mgz |
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?h.ribbon.mgz |
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label/?h.aparc.a2005s.annot |
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-wmparc |
aparc+aseg.mgz |
mri_aparc2aseg --s <subjid> --labelwm --hypo-as-wm --rip-unknown --ribbon --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz |
wmparc.mgz |
|
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 |