#acl LcnGroup:read,write,delete,revert All:read

== FreeSurfer Tutorial: Process Flow ==
This table shows the recon-all steps for stable version 5.3 of FreeSurfer.

See also the OtherUsefulFlags for other recon-all options.

||'''recon-all step''' ||'''Individual Flag''' ||'''Input''' ||'''Command Line''' ||'''Output''' ||
||<style="text-align: left;" |17>'''[[recon-all]] -autorecon1 -subjid <subjid>''' ||
||<style="text-align: left;" |2>-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 ||
||<style="text-align: left;" |4>-[[motioncor]] ||orig/001.mgz ||<style="text-align: left;" |2>[[mri_robust_template]] --mov 001.mgz 002.mgz --average 1 --template rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --subsample 200||<style="text-align: left;" |2>rawavg.mgz ||
||orig/002.mgz ||
||rawavg.mgz ||[[mri_convert]] rawavg.mgz orig.mgz --conform ||orig.mgz ||
||orig.mgz ||[[mri_add_xform_to_header]] -c transforms/talairach.xfm orig.mgz orig.mgz ||orig.mgz ||
||<style="text-align: left;" |5>-[[talairach]] || 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 ||
||orig_nu.mgz ||[[talairach_avi]] --i orig_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 ||
||transforms/talairach.xfm ||[[talairach_afd]] -T 0.005 -xfm transforms/talairach.xfm ||transforms/talairach.xfm ||
|| ||awk -f $FREESURFER_HOME/bin/extract_talairach_avi_QA.awk transforms/talairach_avi.log ||transforms/talairach_avi.log ||
||-[[nuintensitycor]] ||orig.mgz, talairach.xfm ||[[mri_nu_correct.mni]] --i orig.mgz --o nu.mgz --n 2 --uchar transforms/talairach.xfm||nu.mgz ||
||-[[normalization]] ||nu.mgz ||[[mri_normalize]] -g 1 nu.mgz T1.mgz ||T1.mgz ||
||<style="text-align: left;" |3>-[[skullstrip]] ||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 ||
||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 ||
||brainmask.auto.mgz ||cp brainmask.auto.mgz brainmask.mgz ||brainmask.mgz ||
|| || || || ||
||<style="text-align: left;" |61>'''[[recon-all]] -autorecon2 -subjid <subjid>''' ||
||<style="text-align: left;" |2>-[[gcareg]] ||brainmask.mgz ||<style="text-align: left;" |2>[[mri_em_register]] -uns 3 -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB_all_2008-03-26.gca transforms/talairach.lta ||<style="text-align: left;" |2>transforms/talairach.lta ||
||nu.mgz ||
||<style="text-align: left;" |3>-[[canorm]] ||brainmask.mgz ||<style="text-align: left;" |3>[[mri_ca_normalize]] -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz ||<style="text-align: left;" |3>norm.mgz ||
||nu.mgz ||
||transforms/talairach.lta ||
||<style="text-align: left;" |3>-[[careg]] ||brainmask.mgz ||<style="text-align: left;" |3>[[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 ||<style="text-align: left;" |3>transforms/talairach.m3z ||
||transforms/talairach.lta ||
||norm.mgz ||
||<style="text-align: left;" |3>-[[careginv]] ||<style="text-align: left;" |3>transforms/talairach.m3z ||<style="text-align: left;" |3>[[mri_ca_register]] -invert-and-save transforms/talairach.m3z ||transforms/talairach.m3z.inv.x.mgz ||
||transforms/talairach.m3z.inv.y.mgz ||
||transforms/talairach.m3z.inv.z.mgz ||
||<style="text-align: left;" |2>-[[rmneck]] ||nu.mgz ||<style="text-align: left;" |2>[[mri_remove_neck]] -radius 25 nu.mgz transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2008-03-26.gca nu_noneck.mgz ||<style="text-align: left;" |2>nu_noneck.mgz ||
||transforms/talairach.m3z ||
||<style="text-align: left;" |2>-[[skull-lta]] ||transforms/talairach.lta ||<style="text-align: left;" |2>[[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 ||<style="text-align: left;" |2>transforms/talairach_with_skull.lta ||
||nu_noneck.mgz ||
||<style="text-align: left;" |4>-[[calabel]] ||norm.mgz ||<style="text-align: left;" |2>[[mri_ca_label]] -align norm.mgz transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz ||<style="text-align: left;" |2>aseg.auto_noCCseg.mgz ||
||transforms/talairach.m3z ||
||aseg.auto_noCCseg.mgz ||<style="text-align: left;" |1>[[mri_cc]] -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz <subjid> ||aseg.auto.mgz ||
||aseg.auto.mgz ||cp aseg.auto.mgz aseg.mgz ||aseg.mgz ||
||<style="text-align: left;" |3>-[[normalization2]] ||brainmask.mgz ||<style="text-align: left;" |3>[[mri_normalize]] -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz ||<style="text-align: left;" |3>brain.mgz ||
||norm.mgz ||
||aseg.mgz ||
||<style="text-align: left;" |2>-[[maskbfs]] ||brain.mgz ||<style="text-align: left;" |2>[[mri_mask]] -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz ||<style="text-align: left;" |2>brain.finalsurfs.mgz ||
||brainmask.mgz ||
||<style="text-align: left;" |6>-[[segmentation]] ||brain.mgz ||[[mri_segment]] brain.mgz wm.seg.mgz ||wm.seg.mgz ||
||wm.seg.mgz ||<style="text-align: left;" |3>[[mri_edit_wm_with_aseg]] -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz ||<style="text-align: left;" |3>wm.asegedit.mgz ||
||aseg.mgz ||
||brain.mgz ||
||wm.asegedit.mgz ||<style="text-align: left;" |2>[[mri_pretess]] wm.asegedit.mgz wm norm.mgz wm.mgz ||<style="text-align: left;" |2>wm.mgz ||
||norm.mgz ||
||<style="text-align: left;" |3>-[[fill]] ||wm.mgz ||<style="text-align: left;" |3>[[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 ||<style="text-align: left;" |2>../scripts/ponscc.cut.log ||
||transforms/talairach.lta ||
||<style="text-align: left;" |8>-[[tessellate]] ||filled.mgz ||<style="text-align: left;" |2>[[mri_pretess]] filled.mgz 255 norm.mgz filled-pretess255.mgz ||<style="text-align: left;" |2>filled-pretess255.mgz ||
||norm.mgz ||
||filled-pretess255.mgz ||[[mri_tessellate]] filled-pretess255.mgz 255 lh.orig.nofix ||lh.orig.nofix ||
||filled.mgz ||<style="text-align: left;" |2>[[mri_pretess]] filled.mgz 127 norm.mgz filled-pretess127.mgz ||<style="text-align: left;" |2>filled-pretess127.mgz ||
||norm.mgz ||
||filled-pretess127.mgz ||[[mri_tessellate]] filled-pretess127.mgz 127 rh.orig.nofix ||rh.orig.nofix ||
||?h.orig.nofix ||mris_extract_main_component ?h.orig.nofix ?h.orig.nofix ||?h.orig.nofix ||
|| ||rm -f filled-pretess255.mgz filled-pretess127.mgz || ||
||-[[smooth|smooth1]] ||?h.orig.nofix ||[[mris_smooth]] -nw ?h.orig.nofix ?h.smoothwm.nofix ||?h.smoothwm.nofix ||
||-[[inflate|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 ||
||<style="text-align: left;" |6>-[[fix]] ||?h.orig.nofix ||cp ?h.orig.nofix ?h.orig ||?h.orig ||
||?h.inflated.nofix ||cp ?h.inflated.nofix ?h.inflated ||?h.inflated ||
||?h.qsphere.nofix ||[[mris_fix_topology]] -mgz -sphere qsphere.nofix -ga <subjid> ?h ||?h.orig ||
||?h.orig ||[[mris_euler_number]] ?h.orig ||?h.orig ||
||?h.orig ||mris_remove_intersection ?h.orig ?h.orig ||?h.orig ||
|| ||rm ?h.inflated || ||
||<style="text-align: left;" |5>-white ||<style="text-align: left;" |1>aseg.mgz, brain.finalsurfs.mgz, wm.mgz, filled.mgz ||<style="text-align: left;" |5>[[mris_make_surfaces]] -whiteonly -noaparc -mgz -T1 brain.finalsurfs <subjid> ?h ||?h.white ||
||<style="text-align: left;" |4>?h.orig ||
||?h.curv ||
||?h.area||
||?h.cortex.label ||
||-[[smooth|smooth2]] ||?h.white ||[[mris_smooth]] -n 3 -nw ?h.white ?h.smoothwm ||?h.smoothwm ||
||<style="text-align: left;" |4>-[[inflate|inflate2]] ||<style="text-align: left;" |2>?h.smoothwm ||<style="text-align: left;" |2>[[mris_inflate]] ?h.smoothwm ?h.inflated ||?h.inflated ||
||<style="text-align: left;">?h.sulc ||
||<style="text-align: left;" |2>?h.inflated ||<style="text-align: left;" |2>[[mris_curvature]] -thresh .999 -n -a 5 -w -distances 10 10 ?h.inflated ||?h.inflated.H ||
||?h.inflated.K ||
|| || || || || ||
||<style="text-align: left;" |36>'''[[recon-all]] -autorecon3 -subjid <subjid>''' ||
||-[[sphere]] ||?h.inflated,?h.smoothwm ||[[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 ||
||<style="text-align: left;" |2>-[[jacobian_white]] ||?h.white ||<style="text-align: left;" |2>[[mris_jacobian]] ?h.white ?h.sphere.reg ?h.jacobian_white ||<style="text-align: left;" |2>?h.jacobian_white ||
||?h.sphere.reg ||
||-[[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 ||
||<style="text-align: left;" |2>-[[cortparc]] ||aseg.mgz, ?h.cortex.label ||<style="text-align: left;" |2>[[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.2010-03-25.gcs ?h.aparc.annot ||<style="text-align: left;" |2>label/?h.aparc.annot ||
||?h.sphere.reg ||
||<style="text-align: left;" |4>-pial ||<style="text-align: left;" |1>aseg.mgz, brain.finalsurfs.mgz, wm.mgz, filled.mgz ||<style="text-align: left;" |4>[[mris_make_surfaces]] -white NOWRITE -mgz -T1 brain.finalsurfs <subjid> ?h ||?h.pial ||
||<style="text-align: left;" |3>?h.orig, label/?h.aparc.annot ||
||?h.curv.pial, ?h.area.pial ||
||?h.thickness||
||<style="text-align: left;" |5>-[[surfvolume]] ||<style="text-align: left;" |1>?h.area ||<style="text-align: left;" |2>[[mris_calc]] -o ?h.area.mid ?h.area add  ?h.area.pial ||<style="text-align: left;" |2>?h.area.mid ||
||?h.area.pial ||
||<style="text-align: left;" |1>?h.area.mid ||<style="text-align: left;" |1>[[mris_calc]] -o ?h.area.mid ?h.area.mid div 2 ||?h.area.mid ||
||<style="text-align: left;" |1>?h.area.mid ||<style="text-align: left;" |2>[[mris_calc]] -o ?h.volume ?h.area.mid mul ?h.thickness ||<style="text-align: left;" |2>?h.volume ||
||?h.thickness ||
||-[[pctsurfcon]] ||rawavg.mgz ||pctsurfcon --s <subjid> -?h-only ||?h.w-c.pct.mgz ||
||-[[parcstats]] ||label/?h.aparc.annot ||[[mris_anatomical_stats]] -mgz -cortex label/?h.cortex.label -f stats/?h.aparc.stats -b -a label/?h.aparc.annot -c label/aparc.annot.ctab <subjid> ?h white ||stats/?h.aparc.stats label/aparc.annot.ctab ||
||<style="text-align: left;" |2>-[[cortparc|cortparc2]] ||aseg.mgz, ?h.cortex.label ||<style="text-align: left;" |2>[[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 ||<style="text-align: left;" |2>label/?h.aparc.a2009s.annot ||
||?h.sphere.reg ||
||-[[parcstats|parcstats2]] ||label/?h.aparc.a2009s.annot ||[[mris_anatomical_stats]] -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 white ||stats/?h.aparc.a2009s.stats stats/aparc.annot.a2009s.ctab ||
||<style="text-align: left;" |3>-[[cortribbon]] ||aseg.mgz ||<style="text-align: left;" |3>[[mris_volmask]] --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance <subjid> ||<style="text-align: left;" |3>?h.ribbon.mgz, ribbon.mgz  ||
||?h.white ||
||?h.pial ||
||-[[segstats]] ||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 ||
||<style="text-align: left;" |6>-[[aparc2aseg]] ||aseg.mgz ||<style="text-align: left;" |3>[[mri_aparc2aseg]] --s <subjid> --ribbon ||<style="text-align: left;" |3>aparc+aseg.mgz ||
||?h.ribbon.mgz||
||label/?h.aparc.annot ||
||aseg.mgz ||<style="text-align: left;" |3>[[mri_aparc2aseg]] --s <subjid> --ribbon --a2009s ||<style="text-align: left;" |3>aparc.a2009s+aseg.mgz ||
||?h.ribbon.mgz ||
||label/?h.aparc.a2009s.annot ||
||<style="text-align: left;" |2>-[[wmparc]] ||aparc+aseg.mgz ||<style="text-align: left;" |1>[[mri_aparc2aseg]] --s <subjid> --labelwm --hypo-as-wm --rip-unknown --ribbon --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz ||<style="text-align: left;" |1>wmparc.mgz ||
||wmparc.mgz ||<style="text-align: left;" |1>[[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 ||<style="text-align: left;" |1>stats/wmparc.stats ||
||-[[BrodmannAreaMaps|balabels]] ||?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||
||-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||
||||||||||<style="text-align: center;"> ||