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Comment: Updated to point to 6.0 as the most stable release
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This table shows the recon-all steps for the current '''dev''' version of FreeSurfer. See [[ReconAllTableStableV5.1]] to see a process flow for the latest '''stable''' version of FreeSurfer.

Click [[ReconAllBlockDiagram|here]] to see this information presented in a block diagram format and [[ReconAllFilesVsSteps|here for a process v. files table]].		 This table shows the recon-all steps for the current '''dev''' version of FreeSurfer [[ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/|(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.
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||'''recon-all step''' ||'''Individual Flag''' ||'''Input''' ||'''Command Line''' ||'''Output''' ||
||<style="text-align:left;" |16>'''[[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 --iscaleout --subsample 200 --lta ||<style="text-align:left;" |2>rawavg.mgz ||		 ||<tablestyle="text-align:left; ;text-align:left">'''recon-all step''' ||'''Individual Flag''' ||'''Input''' ||'''Command Line''' ||'''Output''' ||
||<style="text-align:left" |20>'''[[recon-all]] -autorecon1 -subjid <subjid>''' ||
||<style="text-align:left" |1>-i <invol1> ||invol1.dcm ''or .nii or .mgz'' ||[[mri_convert]] invol1.dcm orig/001.mgz ||orig/001.mgz ||
||<style="text-align:left" |1>-i <invol2> ''optional'' ||invol2.dcm'' or .nii or .mgz'' ||[[mri_convert]] invol2.dcm orig/002.mgz ||orig/002.mgz ||
||<style="text-align:left" |1>-T2 <invol> ''or'' <<BR>> -FLAIR <invol> ''optional'' ||<style="text-align:left" |1>invol.dcm ''or .nii or .mgz'' ||<style="text-align:left" |1>[[mri_convert]] --no_scale 1 invol.dcm orig/T2raw.mgz ||<style="text-align:left" |1>orig/T2raw.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 --iscaleout --subsample 200 --lta ||<style="text-align:left" |2>rawavg.mgz ||
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||<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 || ||<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 ||
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||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 ||
||-[[normalization]] ||orig_nu.mgz ||[[mri_normalize]] -g 1 orig_nu.mgz T1.mgz ||T1.mgz ||
||<style="text-align:left;" |3>-[[skullstrip]] ||orig_nu.mgz ||[[mri_em_register]] -skull orig_nu.mgz $FREESURFER_HOME/average/RB_all_withskull_2014-08-21.gca transforms/talairach_with_skull.lta ||transforms/talairach_with_skull.lta ||
||T1.mgz ||[[mri_watershed]] -T1 -brain_atlas $FREESURFER_HOME/average/RB_all_withskull_2014-08-21.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz ||brainmask.auto.mgz ||		 ||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 ||
||<style="text-align:left;" |2>-[[nuintensitycor]] ||orig.mgz ||<style="text-align:left;" |2>[[mri_nu_correct.mni]] --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 ||<style="text-align:left;" |2>nu.mgz ||
||talairach.xfm ||
||<style="text-align:left" |1>-[[normalization]] ||nu.mgz ||[[mri_normalize]] -g 1 -mprage 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_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 ||
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|| || || || ||
||<style="text-align:left;" |64>'''[[recon-all]] -autorecon2 -subjid <subjid>''' ||
||<style="text-align:left;" |3>-[[nuintensitycor]] ||orig.mgz ||<style="text-align:left;" |3>[[mri_nu_correct.mni]] --i orig.mgz --mask brainmask.mgz --o nu.mgz --n 1 --proto-iters 1000 --uchar transforms/talairach.xfm ||<style="text-align:left;" |3>nu.mgz ||
||brainmask.mgz ||
||talairach.xfm ||
||<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_2014-08-21.gca transforms/talairach.lta ||<style="text-align:left;" |2>transforms/talairach.lta ||

||<tablestyle="text-align:left;        ;text-align:left">'''recon-all step''' ||'''Individual Flag''' ||'''Input''' ||'''Command Line''' ||'''Output''' ||
||<style="text-align:left;" |69>'''[[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_2016-05-10.vc700.gca transforms/talairach.lta ||<style="text-align:left;" |2>transforms/talairach.lta ||
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||<style="text-align:left;" |3>-[[canorm]] ||brainmask.mgz ||<style="text-align:left;" |3>[[mri_ca_normalize]] -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB_all_2014-08-21.gca transforms/talairach.lta norm.mgz ||<style="text-align:left;" |3>norm.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_2016-05-10.vc700.gca transforms/talairach.lta norm.mgz ||<style="text-align:left;" |3>norm.mgz ||
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||<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_2014-08-21.gca transforms/talairach.m3z ||<style="text-align:left;" |3>transforms/talairach.m3z || ||<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_2016-05-10.vc700.gca transforms/talairach.m3z ||<style="text-align:left;" |3>transforms/talairach.m3z ||
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||<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_2014-08-21.gca nu_noneck.mgz ||<style="text-align:left;" |2>nu_noneck.mgz ||		 ||<style="text-align:left;" |4>-[[calabel]] ||norm.mgz ||<style="text-align:left;" |2>[[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 ||<style="text-align:left;" |2>aseg.auto_noCCseg.mgz ||
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||<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_2014-08-21.gca transforms/talairach_with_skull_2.lta ||<style="text-align:left;" |2>transforms/talairach_with_skull_2.lta ||
||nu_noneck.mgz ||
||<style="text-align:left;" |4>-[[calabel]] ||norm.mgz ||<style="text-align:left;" |2>[[mri_ca_label]] -align -nobigventricles norm.mgz transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2014-08-21.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 ||		 ||aseg.auto_noCCseg.mgz ||<style="text-align:left;" |1>[[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 ||
||<style="text-align:left;" |3>-[[normalization2]] ||brainmask.mgz ||<style="text-align:left;" |3>[[mri_normalize]] -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz ||<style="text-align:left;" |3>brain.mgz ||
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||aseg.mgz || ||aseg.presurf.mgz ||
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||<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]] wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz ||<style="text-align:left;" |3>wm.asegedit.mgz ||
||aseg.mgz ||		 ||<style="text-align:left;" |6>-[[segmentation]] ||brain.mgz ||[[mri_segment]] -mprage brain.mgz wm.seg.mgz ||wm.seg.mgz ||
||wm.seg.mgz ||<style="text-align:left;" |3>[[mri_edit_wm_with_aseg]] wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz ||<style="text-align:left;" |3>wm.asegedit.mgz ||
||aseg.presurf.mgz ||
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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_extract_main_component ?h.orig.nofix ?h.orig.nofix ||?h.orig.nofix ||
|| ||rm -f filled-pretess255.mgz filled-pretess127.mgz || ||
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||?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 ||		 ||?h.orig ||mris_remove_intersection ?h.orig ?h.orig ||?h.orig ||
|| ||rm ?h.inflated || ||
||<style="text-align:left;" |8>-white ||<style="text-align:left;" |1>aseg.presurf.mgz ||<style="text-align:left;" |8>[[mris_make_surfaces]] -aseg ../mri/aseg.presurf -whiteonly -noaparc -mgz -T1 brain.finalsurfs <subjid> ?h ||<style="text-align:left" |4>?h.white ||
||<style="text-align:left">brain.finalsurfs.mgz ||
||<style="text-align:left">wm.mgz ||
||<style="text-align:left">filled.mgz ||
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||<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 ||		 ||<style="text-align:left" |2>-[[inflate|inflate2]] ||<style="text-align:left" |2>?h.smoothwm ||<style="text-align:left" |2>[[mris_inflate]] ?h.smoothwm ?h.inflated ||?h.inflated ||
||?h.sulc ||
||<style="text-align:left" |4>-curvHK ||<style="text-align:left" |2>?h.white ||<style="text-align:left" |2>[[mris_curvature]] -w ?h.white ||<style="text-align:left" |1>?h.white.H ||
||?h.white.K ||
||<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 ||<style="text-align:left" |1>?h.inflated.H ||
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|| || || || || ||
||<style="text-align:left;" |41>'''[[recon-all]] -autorecon3 -subjid <subjid>''' ||
||-[[sphere]] ||?h.inflated,?h.smoothwm ||[[mris_sphere]] ?h.inflated ?h.sphere ||?h.sphere ||		 ||<style="text-align:left" |3>-curvstats ||<style="text-align:left">?h.smoothwm ||<style="text-align:left" |3>mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/?h.curv.stats -F smoothwm <subjid> ?h curv sulc ||<style="text-align:left" |3>stats/?h.curv.stats ||
||<style="text-align:left">?h.curv ||
||<style="text-align:left">?h.sulc ||


||<tablestyle="text-align:left; ;text-align:left">'''recon-all step''' ||'''Individual Flag''' ||'''Input''' ||'''Command Line''' ||'''Output''' ||
||<style="text-align:left;" |83>'''[[recon-all]] -autorecon3 -subjid <subjid>''' ||
||<style="text-align:left" |2>-[[sphere]] ||?h.inflated ||<style="text-align:left" |2>[[mris_sphere]] ?h.inflated ?h.sphere ||<style="text-align:left" |2>?h.sphere ||
||<style="text-align:left">?h.smoothwm ||
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||<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.2007-06-20gcs ?h.aparc.annot ||<style="text-align:left;" |2>label/?h.aparc.annot || ||<style="text-align:left;" |3>-[[cortparc]] ||aseg.presurf.mgz ||<style="text-align:left;" |3>[[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 ||<style="text-align:left;" |3>label/?h.aparc.annot ||
||<style="text-align:left">?h.cortex.label ||
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||<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 ||
||-[[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 ||
||<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 -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 ||
||<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 ||		 ||<style="text-align:left;" |8>-pial ||<style="text-align:left;" |1>aseg.presurf.mgz ||<style="text-align:left;" |8>[[mris_make_surfaces]] -orig_white white -orig_pial white -aseg ../mri/aseg.presurf -nowhite -mgz -T1 brain.finalsurfs <subjid> ?h ||<style="text-align:left" |4>?h.pial ||
||brain.finalsurfs.mgz ||
||wm.mgz ||
||filled.mgz ||
||<style="text-align:left;" |3>?h.orig ||
||?h.curv.pial ||
||<style="text-align:left">?h.area.pial ||
||<style="text-align:left" |1>label/?h.aparc.annot ||?h.thickness ||
||<style="text-align:left;" |15>-T2pial ''or'' <<BR>>-FLAIRpial ''optional'' ||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 ||<style="text-align:left" |2>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 ||<style="text-align:left" |2>T2.prenorm.mgz ||
||transforms/T2raw.lta ||
||aseg.presurf.mgz ||<style="text-align:left" |3>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 ||<style="text-align:left" |3>T2.mgz ||
||?h.white ||
||T2.prenorm.mgz ||
||?h.pial ||cp -v surf/?h.pial surf/?h.woT2.pial ||?h.woT2.pial ||
||aseg.presurf.mgz ||<style="text-align:left" |8>[[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 ||<style="text-align:left" |3>?h.pial ||
||brain.finalsurfs.mgz ||
||wm.mgz ||
||filled.mgz ||<style="text-align:left" |2>?h.curv.pial ||
||?h.white ||
||<style="text-align:left" |1>label/?h.aparc.annot ||<style="text-align:left" |1>?h.area.pial ||
||<style="text-align:left" |1>T2.mgz ||<style="text-align:left" |2>?h.thickness ||
||?h.woT2.pial ||
||<style="text-align:left;" |3>-[[cortribbon]] ||aseg.presurf.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 <subjid> ||<style="text-align:left;" |2>?h.ribbon.mgz ||
||?h.white ||
||?h.pial ||<style="text-align:left" |1>ribbon.mgz ||
||<style="text-align:left" |5>-[[parcstats]] ||<style="text-align:left" |1>label/?h.aparc.annot ||<style="text-align:left" |5>[[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 ||
||<style="text-align:left" |1>wm.mgz, ribbon.mgz ||<style="text-align:left" |4>label/aparc.annot.ctab ||
Line 115: Line 134:
||<style="text-align:left;" |2>-[[cortparc|cortparc3]] ||aseg.mgz, ?h.cortex.label ||<style="text-align:left;" |2>[[mris_ca_label]]  ../label/lh.cortex.label -aseg aseg.mgz <subjid> ?h ?h.sphere.reg $FREESURFER_HOME/average/?h.DKTatlas40.gcs ../label/?h.aparc.DKTatlas40.annot ||<style="text-align:left;" |2>label/?h.aparc.a2009s.annot || ||?h.thickness ||
||<style="text-align:left;" |3>-[[cortparc|cortparc2]] ||aseg.presurf.mgz ||<style="text-align:left;" |3>[[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 ||<style="text-align:left;" |3>label/?h.aparc.a2009s.annot ||
Line 117: Line 137:
||-[[parcstats|parcstats3]] ||label/?h.aparc.a2009s.annot ||[[mris_anatomical_stats]] -mgz -f stats/?h.aparc.DKTatlas.stats -b -a label/?h.aparc.DKTatlas.annot -c label/aparc.annot.DKTatlas.ctab <subjid> ?h ||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 ||		 ||label/?h.cortex.label ||
||<style="text-align:left" |5>-[[parcstats|parcstats2]] ||<style="text-align:left" |1>label/?h.aparc.a2009s.annot ||<style="text-align:left" |5>[[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 ||
||<style="text-align:left" |1>wm.mgz, ribbon.mgz ||<style="text-align:left" |4>label/aparc.annot.a2009s.ctab ||
Line 121: Line 142:
||-[[segstats]] ||aseg.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 ||
||<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.thickness ||
||<style="text-align:left;" |3>-[[cortparc|cortparc3]] ||aseg.presurf.mgz ||<style="text-align:left;" |3>[[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 ||<style="text-align:left;" |3>label/?h.aparc.DKTatlas.annot ||
||?h.sphere.reg ||
||label/?h.cortex.label ||
||<style="text-align:left" |5>-[[parcstats|parcstats3]] ||<style="text-align:left" |1>label/?h.aparc.DKTatlas.annot ||<style="text-align:left" |5>[[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 ||
||<style="text-align:left" |1>wm.mgz, ribbon.mgz ||<style="text-align:left" |4>label/aparc.annot.DKTatlas.ctab ||
||?h.white ||
||?h.pial ||
||?h.thickness ||
||<style="text-align:left;" |4>-pctsurfcon ||rawavg.mgz ||<style="text-align:left;" |4>pctsurfcon --s <subjid> --?h-only ||<style="text-align:left;" |2>?h.w-g.pct.mgh ||
||orig.mgz ||
||?h.cortex.label ||<style="text-align:left" |2>stats/?h.w-g.pct.stats ||
||?h.white ||
||<style="text-align:left" |2>-hyporelabel ||<style="text-align:left" |1>aseg.presurf.mgz ||<style="text-align:left" |2>mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz ||<style="text-align:left" |2>aseg.presurf.hypos.mgz ||
||?h.white ||
||<style="text-align:left;" |12>-[[aparc2aseg]] ||aseg.presurf.hypos.mgz ||<style="text-align:left;" |4>[[mri_aparc2aseg]] --s <subjid> --ribbon ||<style="text-align:left;" |4>aparc+aseg.mgz ||
Line 125: Line 160:
||aseg.mgz ||<style="text-align:left;" |3>[[mri_aparc2aseg]] --s <subjid> --ribbon --a2009s ||<style="text-align:left;" |3>aparc.a2009s+aseg.mgz || ||<style="text-align:left">ribbon.mgz ||
||aseg.presurf.hypos.mgz ||<style="text-align:left;" |4>[[mri_aparc2aseg]] --s <subjid> --ribbon --annot aparc.a2009s ||<style="text-align:left;" |4>aparc.a2009s+aseg.mgz ||
Line 128: Line 164:
||<style="text-align:left">ribbon.mgz ||
||aseg.presurf.hypos.mgz ||<style="text-align:left;" |4>[[mri_aparc2aseg]] --s <subjid> --ribbon --annot aparc.DKTatlas ||<style="text-align:left;" |4>aparc.DKTatlas+aseg.mgz ||
||?h.ribbon.mgz ||
||label/?h.aparc.DKTatlas.annot ||
||<style="text-align:left">ribbon.mgz ||
||<style="text-align:left;" |1>-apas2aseg ||aparc+aseg.mgz ||<style="text-align:left;" |1>apas2aseg --i aparc+aseg.mgz --o aseg.mgz ||<style="text-align:left;" |1>aseg.mgz ||
||<style="text-align:left" |2>-[[segstats]] ||brainmask.mgz, norm.mgz, aseg.mgz, aseg.presurf.mgz, ribbon.mgz ||<style="text-align:left" |2>[[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> ||<style="text-align:left" |2>stats/aseg.stats ||
||?h.orig.nofix, ?h.white, ?h.pial ||
Line 129: Line 173:
||wmparc.mgz ||<style="text-align:left;" |1>[[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 ||<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;"> ||		 ||talairach.xfm, brainmask.mgz, norm.mgz, ribbon.mgz, wmparc.mgz, aseg.presurf.mgz, ?h.white, ?h.pial ||<style="text-align:left;" |1>[[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 ||<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*_exvivo.label label/?h.perirhinal_exvivo.label label/?h.entorhinal_exvivo.label ||

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>

-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
-FLAIR <invol> optional

invol.dcm or .nii or .mgz

mri_convert --no_scale 1 invol.dcm orig/T2raw.mgz

orig/T2raw.mgz

-motioncor

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

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

-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

awk -f $FREESURFER_HOME/bin/extract_talairach_avi_QA.awk transforms/talairach_avi.log

transforms/talairach_avi.log

-nuintensitycor

orig.mgz

mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2

nu.mgz

talairach.xfm

-normalization

nu.mgz

mri_normalize -g 1 -mprage nu.mgz T1.mgz

T1.mgz

-skullstrip

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>

-gcareg

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

-canorm

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

nu.mgz

transforms/talairach.lta

-careg

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

transforms/talairach.lta

norm.mgz

-calabel

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

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

-normalization2

brainmask.mgz

mri_normalize -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz

brain.mgz

norm.mgz

aseg.presurf.mgz

-maskbfs

brain.mgz

mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz

brain.finalsurfs.mgz

brainmask.mgz

-segmentation

brain.mgz

mri_segment -mprage brain.mgz wm.seg.mgz

wm.seg.mgz

wm.seg.mgz

mri_edit_wm_with_aseg wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz

wm.asegedit.mgz

aseg.presurf.mgz

brain.mgz

wm.asegedit.mgz

mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz

wm.mgz

norm.mgz

-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

transforms/talairach.lta

-tessellate

filled.mgz

mri_pretess filled.mgz 255 norm.mgz filled-pretess255.mgz

filled-pretess255.mgz

norm.mgz

filled-pretess255.mgz

mri_tessellate filled-pretess255.mgz 255 lh.orig.nofix

lh.orig.nofix

filled.mgz

mri_pretess filled.mgz 127 norm.mgz filled-pretess127.mgz

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

-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

?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

-white

aseg.presurf.mgz

mris_make_surfaces -aseg ../mri/aseg.presurf -whiteonly -noaparc -mgz -T1 brain.finalsurfs <subjid> ?h

?h.white

brain.finalsurfs.mgz

wm.mgz

filled.mgz

?h.orig

?h.curv

?h.area

?h.cortex.label

-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

?h.sulc

-curvHK

?h.white

mris_curvature -w ?h.white

?h.white.H

?h.white.K

?h.inflated

mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ?h.inflated

?h.inflated.H

?h.inflated.K

-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

?h.sulc

recon-all step

Individual Flag

Input

Command Line

Output

recon-all -autorecon3 -subjid <subjid>

-sphere

?h.inflated

mris_sphere ?h.inflated ?h.sphere

?h.sphere

?h.smoothwm

-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

-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.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

?h.cortex.label

?h.sphere.reg

-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

wm.mgz

filled.mgz

?h.orig

?h.curv.pial

?h.area.pial

label/?h.aparc.annot

?h.thickness

-T2pial or
-FLAIRpial optional

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

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

?h.white

T2.prenorm.mgz

?h.pial

cp -v surf/?h.pial surf/?h.woT2.pial

?h.woT2.pial

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

brain.finalsurfs.mgz

wm.mgz

filled.mgz

?h.curv.pial

?h.white

label/?h.aparc.annot

?h.area.pial

T2.mgz

?h.thickness

?h.woT2.pial

-cortribbon

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

?h.white

?h.pial

ribbon.mgz

-parcstats

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

wm.mgz, ribbon.mgz

label/aparc.annot.ctab

?h.white

?h.pial

?h.thickness

-cortparc2

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

?h.sphere.reg

label/?h.cortex.label

-parcstats2

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

?h.white

?h.pial

?h.thickness

-cortparc3

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

-parcstats3

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

-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

-aparc2aseg

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

-segstats

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

-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

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

-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*_exvivo.label label/?h.perirhinal_exvivo.label label/?h.entorhinal_exvivo.label

ReconAllDevTable (last edited 2017-02-17 11:53:55 by LeeTirrell)