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————————————————————————————————— = ReconAllTableStable7.1.1 = This table shows the recon-all steps for the '''stable''', publicly released, '''version 7.1.1 '''of !FreeSurfer [[DownloadAndInstall | (available here)]]. See also the [[https://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags|OtherUsefulFlags]] for other recon-all options. ||<tablestyle="text-align:left; ;text-align:left">'''recon-all step''' ||'''Individual Flag''' ||'''Input''' ||'''Command Line''' ||'''Output''' || ||<style="text-align:left" |20>'''[[https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all|recon-all]] -autorecon1 -subjid <subjid>''' || ||<style="text-align:left" |1>-i <invol1> ||invol1.dcm ''or .nii or .mgz'' ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_convert|mri_convert]] invol1.dcm orig/001.mgz ||orig/001.mgz || ||<style="text-align:left" |1>-i <invol2> ''optional'' ||invol2.dcm'' or .nii or .mgz'' ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_convert|mri_convert]] invol2.dcm orig/002.mgz ||orig/002.mgz || ||<style="text-align:left" |1>-T2 <invol> ''or'' -FLAIR <invol> ''optional'' ||<style="text-align:left" |1>invol.dcm ''or .nii or .mgz'' ||<style="text-align:left" |1>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_convert|mri_convert]] --no_scale 1 invol.dcm orig/T2raw.mgz ''(or orig/FLAIRraw.mgz)'' ||<style="text-align:left" |1>orig/T2raw.mgz ''(or orig/FLAIRraw.mgz)'' || ||<style="text-align:left" |4>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/motioncor|motioncor]] ||orig/001.mgz ||<style="text-align:left" |2>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_robust_template|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 || ||orig/002.mgz || ||rawavg.mgz ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_convert|mri_convert]] rawavg.mgz orig.mgz --conform ||orig.mgz || ||orig.mgz ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_add_xform_to_header|mri_add_xform_to_header]] -c transforms/talairach.xfm orig.mgz orig.mgz ||orig.mgz || ||<style="text-align:left" |5>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/talairach|talairach]] ||orig.mgz ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_nu_correct.mni|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 ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/talairach_avi|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 ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/talairach_afd|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>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/nuintensitycor|nuintensitycor]] ||orig.mgz ||<style="text-align:left;" |2>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_nu_correct.mni|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>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/normalization|normalization]] ||nu.mgz ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_normalize|mri_normalize]] -g 1 -mprage nu.mgz T1.mgz ||T1.mgz || ||<style="text-align:left" |3>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/skullstrip|skullstrip]] ||nu.mgz ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_em_register|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 ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_watershed|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 || ||<tablestyle="text-align:left; ;text-align:left">'''recon-all step''' ||'''Individual Flag''' ||'''Input''' ||'''Command Line''' ||'''Output''' || ||<style="text-align:left;" |69>'''[[https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all|recon-all]] -autorecon2 -subjid <subjid>''' || ||<style="text-align:left;" |2>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/gcareg|gcareg]] ||brainmask.mgz ||<style="text-align:left;" |2>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_em_register|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 || ||nu.mgz || ||<style="text-align:left;" |3>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/canorm|canorm]] ||brainmask.mgz ||<style="text-align:left;" |3>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_ca_normalize|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 || ||nu.mgz || ||transforms/talairach.lta || ||<style="text-align:left;" |3>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/careg|careg]] ||brainmask.mgz ||<style="text-align:left;" |3>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_ca_register|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 || ||transforms/talairach.lta || ||norm.mgz || ||<style="text-align:left;" |4>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/calabel|calabel]] ||norm.mgz ||<style="text-align:left;" |2>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_ca_label|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 || ||transforms/talairach.m3z || ||aseg.auto_noCCseg.mgz ||<style="text-align:left;" |1>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_cc|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>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/normalization2|normalization2]] ||brainmask.mgz ||<style="text-align:left;" |3>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_normalize|mri_normalize]] -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz ||<style="text-align:left;" |3>brain.mgz || ||norm.mgz || ||aseg.presurf.mgz || ||<style="text-align:left;" |2>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/maskbfs|maskbfs]] ||brain.mgz ||<style="text-align:left;" |2>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_mask|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>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/segmentation|segmentation]] ||brain.mgz ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segment|mri_segment]] -mprage brain.mgz wm.seg.mgz ||wm.seg.mgz || ||wm.seg.mgz ||<style="text-align:left;" |3>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_edit_wm_with_aseg|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 || ||brain.mgz || ||wm.asegedit.mgz ||<style="text-align:left;" |2>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_pretess|mri_pretess]] wm.asegedit.mgz wm norm.mgz wm.mgz ||<style="text-align:left;" |2>wm.mgz || ||norm.mgz || ||<style="text-align:left;" |3>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/fill|fill]] ||wm.mgz ||<style="text-align:left;" |3>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_fill|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>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/tessellate|tessellate]] ||filled.mgz ||<style="text-align:left;" |2>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_pretess|mri_pretess]] filled.mgz 255 norm.mgz filled-pretess255.mgz ||<style="text-align:left;" |2>filled-pretess255.mgz || ||norm.mgz || ||filled-pretess255.mgz ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_tessellate|mri_tessellate]] filled-pretess255.mgz 255 lh.orig.nofix ||lh.orig.nofix || ||filled.mgz ||<style="text-align:left;" |2>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_pretess|mri_pretess]] filled.mgz 127 norm.mgz filled-pretess127.mgz ||<style="text-align:left;" |2>filled-pretess127.mgz || ||norm.mgz || ||filled-pretess127.mgz ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_tessellate|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 || || ||-[[https://surfer.nmr.mgh.harvard.edu/fswiki/smooth|smooth1]] ||?h.orig.nofix ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_smooth|mris_smooth]] -nw ?h.orig.nofix ?h.smoothwm.nofix ||?h.smoothwm.nofix || ||-[[https://surfer.nmr.mgh.harvard.edu/fswiki/inflate|inflate1]] ||?h.smoothwm.nofix ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_inflate|mris_inflate]] -no-save-sulc ?h.smoothwm.nofix ?h.inflated.nofix ||?h.inflated.nofix || ||-[[https://surfer.nmr.mgh.harvard.edu/fswiki/qsphere|qsphere]] ||?h.inflated.nofix ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_sphere|mris_sphere]] -q ?h.inflated.nofix ?h.qsphere.nofix ||?h.qsphere.nofix || ||<style="text-align:left;" |6>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/fix|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 ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_fix_topology|mris_fix_topology]] -mgz -sphere qsphere.nofix -ga <subjid> ?h ||?h.orig || ||?h.orig ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_euler_number|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;" |8>-white ||<style="text-align:left;" |1>aseg.presurf.mgz ||<style="text-align:left;" |8>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_make_surfaces|mris_make_surfaces]] -aseg ../mri/aseg.presurf -whiteonly -noaparc -mgz -T1 brain.finalsurfs <subjid> ?h ||<style="text-align:left" |4>?h.white.preaparc || ||<style="text-align:left">brain.finalsurfs.mgz || ||<style="text-align:left">wm.mgz || ||<style="text-align:left">filled.mgz || ||<style="text-align:left;" |4>?h.orig || ||?h.curv || ||?h.area || ||?h.cortex.label || ||-[[https://surfer.nmr.mgh.harvard.edu/fswiki/smooth|smooth2]] ||?h.white.preaparc ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_smooth|mris_smooth]] -n 3 -nw ?h.white.preaparc ?h.smoothwm ||?h.smoothwm || ||<style="text-align:left" |2>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/inflate|inflate2]] ||<style="text-align:left" |2>?h.smoothwm ||<style="text-align:left" |2>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_inflate|mris_inflate]] ?h.smoothwm ?h.inflated ||?h.inflated || ||?h.sulc || ||<style="text-align:left" |4>-curvHK ||<style="text-align:left" |2>?h.white.preaparc ||<style="text-align:left" |2>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_curvature|mris_curvature]] -w ?h.white.preaparc ||<style="text-align:left" |1>?h.white.H || ||?h.white.K || ||<style="text-align:left" |2>?h.inflated ||<style="text-align:left" |2>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_curvature|mris_curvature]] -thresh .999 -n -a 5 -w -distances 10 10 ?h.inflated ||<style="text-align:left" |1>?h.inflated.H || ||?h.inflated.K || ||<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;" |85>'''[[https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all|recon-all]] -autorecon3 -subjid <subjid>''' || ||<style="text-align:left" |2>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/sphere|sphere]] ||?h.inflated ||<style="text-align:left" |2>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_sphere|mris_sphere]] ?h.inflated ?h.sphere ||<style="text-align:left" |2>?h.sphere || ||<style="text-align:left">?h.smoothwm || ||-[[https://surfer.nmr.mgh.harvard.edu/fswiki/surfreg|surfreg]] ||?h.sphere ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_register|mris_register]] -curv ?h.sphere $FREESURFER_HOME/average/?h.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ?h.sphere.reg ||?h.sphere.reg || ||<style="text-align:left;" |2>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/jacobian_white|jacobian_white]] ||?h.white.preaparc ||<style="text-align:left;" |2>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_jacobian|mris_jacobian]] ?h.white.preaparc ?h.sphere.reg ?h.jacobian_white ||<style="text-align:left;" |2>?h.jacobian_white || ||?h.sphere.reg || ||-[[https://surfer.nmr.mgh.harvard.edu/fswiki/avgcurv|avgcurv]] ||?h.sphere.reg ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mrisp_paint|mrisp_paint]] -a 5 $FREESURFER_HOME/average/?h.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ?h.sphere.reg ?h.avg_curv ||?h.avg_curv || ||<style="text-align:left;" |3>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/cortparc|cortparc]] ||aseg.presurf.mgz ||<style="text-align:left;" |3>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_ca_label|mris_ca_label]] -l ../label/?h.cortex.label -aseg mri/aseg.presurf.mgz <subjid> ?h ?h.sphere.reg $FREESURFER_HOME/average/?h.curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs ?h.aparc.annot ||<style="text-align:left;" |3>label/?h.aparc.annot || ||<style="text-align:left">?h.cortex.label || ||?h.sphere.reg || ||<style="text-align:left;" |8>-pial ||<style="text-align:left;" |1>aseg.presurf.mgz ||<style="text-align:left;" |8>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_make_surfaces|mris_make_surfaces]] -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -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;" |17>-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 float -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.norm.mgz ||<style="text-align:left" |3>T2.norm.mgz || ||?h.white || ||T2.prenorm.mgz || ||T2.norm.mgz ||<style="text-align:center" |2>mri_mask mri/T2.norm.mgz mri/brainmask.mgz mri/T2.mgz ||<style="text-align:center" |2>T2.mgz || ||brainmask.mgz || ||?h.pial ||cp -v surf/?h.pial surf/?h.woT2.pial ||?h.woT2.pial || ||aseg.presurf.mgz ||<style="text-align:left" |9>[[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" |3>?h.thickness || ||?h.woT2.pial || || || ||<style="text-align:left;" |3>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/cortribbon|cortribbon]] ||aseg.presurf.mgz ||<style="text-align:left" |3>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_volmask|mris_volmask]] --aseg_name aseg.presurf --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>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/parcstats|parcstats]] ||<style="text-align:left" |1>label/?h.aparc.annot ||<style="text-align:left" |5>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_anatomical_stats|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 <white or pial> ||stats/?h.aparc.stats || ||<style="text-align:left" |1>wm.mgz, ribbon.mgz ||<style="text-align:left" |4>label/aparc.annot.ctab || ||?h.white || ||?h.pial || ||?h.thickness || ||<style="text-align:left;" |3>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/cortparc|cortparc2]] ||aseg.presurf.mgz ||<style="text-align:left;" |3>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_ca_label|mris_ca_label]] -l ../label/?h.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 || ||?h.sphere.reg || ||label/?h.cortex.label || ||<style="text-align:left" |5>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/parcstats|parcstats2]] ||<style="text-align:left" |1>label/?h.aparc.a2009s.annot ||<style="text-align:left" |5>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_anatomical_stats|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 || ||?h.white || ||?h.pial || ||?h.thickness || ||<style="text-align:left;" |3>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/cortparc|cortparc3]] ||aseg.presurf.mgz ||<style="text-align:left;" |3>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_ca_label|mris_ca_label]] -l ../label/?h.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>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/parcstats|parcstats3]] ||<style="text-align:left" |1>label/?h.aparc.DKTatlas.annot ||<style="text-align:left" |5>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mris_anatomical_stats|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>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/aparc2aseg|aparc2aseg]] ||aseg.presurf.hypos.mgz ||<style="text-align:left;" |4>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_aparc2aseg|mri_aparc2aseg]] --s <subjid> --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt ||<style="text-align:left;" |4>aparc+aseg.mgz || ||?h.ribbon.mgz || ||label/?h.aparc.annot || ||<style="text-align:left">ribbon.mgz || ||aseg.presurf.hypos.mgz ||<style="text-align:left;" |4>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_aparc2aseg|mri_aparc2aseg]] --s <subjid> --volmask --annot aparc.a2009s --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt ||<style="text-align:left;" |4>aparc.a2009s+aseg.mgz || ||?h.ribbon.mgz || ||label/?h.aparc.a2009s.annot || ||<style="text-align:left">ribbon.mgz || ||aseg.presurf.hypos.mgz ||<style="text-align:left;" |4>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_aparc2aseg|mri_aparc2aseg]] --s <subjid> --volmask --annot aparc.DKTatlas --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt ||<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>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/segstats|segstats]] ||brainmask.mgz, norm.mgz, aseg.mgz, aseg.presurf.mgz, ribbon.mgz ||<style="text-align:left" |2>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats|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 --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 || ||<style="text-align:left;" |2>-[[https://surfer.nmr.mgh.harvard.edu/fswiki/wmparc|wmparc]] ||aparc+aseg.mgz ||<style="text-align:left;" |1>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_aparc2aseg|mri_aparc2aseg]] --s <subjid> --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz ||<style="text-align:left;" |1>wmparc.mgz || ||talairach.xfm, brainmask.mgz, norm.mgz, ribbon.mgz, wmparc.mgz, aseg.presurf.mgz, ?h.white, ?h.pial ||<style="text-align:left;" |1>[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats|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/WMParcStatsLUT.txt ||<style="text-align:left;" |1>stats/wmparc.stats || ||-[[https://surfer.nmr.mgh.harvard.edu/fswiki/BrodmannAreaMaps|balabels]] ||?h.sphere.reg ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/mri_label2label|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 || |
This table shows the recon-all steps for the stable, publicly released, version 6.0 of FreeSurfer (available here).
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 (or orig/FLAIRraw.mgz) |
orig/T2raw.mgz (or orig/FLAIRraw.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 |
||
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 |
||
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 |
||
orig.mgz |
mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 |
nu.mgz |
||
talairach.xfm |
||||
nu.mgz |
mri_normalize -g 1 -mprage nu.mgz T1.mgz |
T1.mgz |
||
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> |
||||
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 |
||
nu.mgz |
||||
transforms/talairach.lta |
||||
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 |
||||
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 |
||
brainmask.mgz |
mri_normalize -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz |
brain.mgz |
||
norm.mgz |
||||
aseg.presurf.mgz |
||||
brain.mgz |
mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz |
brain.finalsurfs.mgz |
||
brainmask.mgz |
||||
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 |
||||
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 |
|
||
?h.orig.nofix |
mris_smooth -nw ?h.orig.nofix ?h.smoothwm.nofix |
?h.smoothwm.nofix |
||
?h.smoothwm.nofix |
mris_inflate -no-save-sulc ?h.smoothwm.nofix ?h.inflated.nofix |
?h.inflated.nofix |
||
?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.preaparc |
|
brain.finalsurfs.mgz |
||||
wm.mgz |
||||
filled.mgz |
||||
?h.orig |
||||
?h.curv |
||||
?h.area |
||||
?h.cortex.label |
||||
?h.white.preaparc |
mris_smooth -n 3 -nw ?h.white.preaparc ?h.smoothwm |
?h.smoothwm |
||
?h.smoothwm |
mris_inflate ?h.smoothwm ?h.inflated |
?h.inflated |
||
?h.sulc |
||||
-curvHK |
?h.white.preaparc |
mris_curvature -w ?h.white.preaparc |
?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> |
||||
?h.inflated |
mris_sphere ?h.inflated ?h.sphere |
?h.sphere |
||
?h.smoothwm |
||||
?h.sphere |
mris_register -curv ?h.sphere $FREESURFER_HOME/average/?h.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ?h.sphere.reg |
?h.sphere.reg |
||
?h.white.preaparc |
mris_jacobian ?h.white.preaparc ?h.sphere.reg ?h.jacobian_white |
?h.jacobian_white |
||
?h.sphere.reg |
||||
?h.sphere.reg |
mrisp_paint -a 5 $FREESURFER_HOME/average/?h.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ?h.sphere.reg ?h.avg_curv |
?h.avg_curv |
||
aseg.presurf.mgz |
mris_ca_label -l ../label/?h.cortex.label -aseg mri/aseg.presurf.mgz <subjid> ?h ?h.sphere.reg $FREESURFER_HOME/average/?h.curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs ?h.aparc.annot |
label/?h.aparc.annot |
||
?h.cortex.label |
||||
?h.sphere.reg |
||||
-pial |
aseg.presurf.mgz |
mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -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 |
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 float -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.norm.mgz |
T2.norm.mgz |
||
?h.white |
||||
T2.prenorm.mgz |
||||
T2.norm.mgz |
mri_mask mri/T2.norm.mgz mri/brainmask.mgz mri/T2.mgz |
T2.mgz |
||
brainmask.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 |
||||
|
||||
aseg.presurf.mgz |
mris_volmask --aseg_name aseg.presurf --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 |
|||
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 <white or pial> |
stats/?h.aparc.stats |
||
wm.mgz, ribbon.mgz |
label/aparc.annot.ctab |
|||
?h.white |
||||
?h.pial |
||||
?h.thickness |
||||
aseg.presurf.mgz |
mris_ca_label -l ../label/?h.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 |
||||
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 |
||||
aseg.presurf.mgz |
mris_ca_label -l ../label/?h.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 |
||||
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 |
||||
aseg.presurf.hypos.mgz |
mri_aparc2aseg --s <subjid> --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt |
aparc+aseg.mgz |
||
?h.ribbon.mgz |
||||
label/?h.aparc.annot |
||||
ribbon.mgz |
||||
aseg.presurf.hypos.mgz |
mri_aparc2aseg --s <subjid> --volmask --annot aparc.a2009s --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt |
aparc.a2009s+aseg.mgz |
||
?h.ribbon.mgz |
||||
label/?h.aparc.a2009s.annot |
||||
ribbon.mgz |
||||
aseg.presurf.hypos.mgz |
mri_aparc2aseg --s <subjid> --volmask --annot aparc.DKTatlas --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt |
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 --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 --volmask --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/WMParcStatsLUT.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 |
—————————————————————————————————
ReconAllTableStable7.1.1
This table shows the recon-all steps for the stable, publicly released, version 7.1.1 of FreeSurfer (available here).
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 (or orig/FLAIRraw.mgz) |
orig/T2raw.mgz (or orig/FLAIRraw.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 |
||
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 |
||
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 |
||
orig.mgz |
mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 |
nu.mgz |
||
talairach.xfm |
||||
nu.mgz |
mri_normalize -g 1 -mprage nu.mgz T1.mgz |
T1.mgz |
||
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> |
||||
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 |
||
nu.mgz |
||||
transforms/talairach.lta |
||||
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 |
||||
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 |
||
brainmask.mgz |
mri_normalize -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz |
brain.mgz |
||
norm.mgz |
||||
aseg.presurf.mgz |
||||
brain.mgz |
mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz |
brain.finalsurfs.mgz |
||
brainmask.mgz |
||||
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 |
||||
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 |
|
||
?h.orig.nofix |
mris_smooth -nw ?h.orig.nofix ?h.smoothwm.nofix |
?h.smoothwm.nofix |
||
?h.smoothwm.nofix |
mris_inflate -no-save-sulc ?h.smoothwm.nofix ?h.inflated.nofix |
?h.inflated.nofix |
||
?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.preaparc |
|
brain.finalsurfs.mgz |
||||
wm.mgz |
||||
filled.mgz |
||||
?h.orig |
||||
?h.curv |
||||
?h.area |
||||
?h.cortex.label |
||||
?h.white.preaparc |
mris_smooth -n 3 -nw ?h.white.preaparc ?h.smoothwm |
?h.smoothwm |
||
?h.smoothwm |
mris_inflate ?h.smoothwm ?h.inflated |
?h.inflated |
||
?h.sulc |
||||
-curvHK |
?h.white.preaparc |
mris_curvature -w ?h.white.preaparc |
?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> |
||||
?h.inflated |
mris_sphere ?h.inflated ?h.sphere |
?h.sphere |
||
?h.smoothwm |
||||
?h.sphere |
mris_register -curv ?h.sphere $FREESURFER_HOME/average/?h.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ?h.sphere.reg |
?h.sphere.reg |
||
?h.white.preaparc |
mris_jacobian ?h.white.preaparc ?h.sphere.reg ?h.jacobian_white |
?h.jacobian_white |
||
?h.sphere.reg |
||||
?h.sphere.reg |
mrisp_paint -a 5 $FREESURFER_HOME/average/?h.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ?h.sphere.reg ?h.avg_curv |
?h.avg_curv |
||
aseg.presurf.mgz |
mris_ca_label -l ../label/?h.cortex.label -aseg mri/aseg.presurf.mgz <subjid> ?h ?h.sphere.reg $FREESURFER_HOME/average/?h.curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs ?h.aparc.annot |
label/?h.aparc.annot |
||
?h.cortex.label |
||||
?h.sphere.reg |
||||
-pial |
aseg.presurf.mgz |
mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -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 |
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 float -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.norm.mgz |
T2.norm.mgz |
||
?h.white |
||||
T2.prenorm.mgz |
||||
T2.norm.mgz |
mri_mask mri/T2.norm.mgz mri/brainmask.mgz mri/T2.mgz |
T2.mgz |
||
brainmask.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 |
||||
|
||||
aseg.presurf.mgz |
mris_volmask --aseg_name aseg.presurf --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 |
|||
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 <white or pial> |
stats/?h.aparc.stats |
||
wm.mgz, ribbon.mgz |
label/aparc.annot.ctab |
|||
?h.white |
||||
?h.pial |
||||
?h.thickness |
||||
aseg.presurf.mgz |
mris_ca_label -l ../label/?h.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 |
||||
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 |
||||
aseg.presurf.mgz |
mris_ca_label -l ../label/?h.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 |
||||
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 |
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wm.mgz, ribbon.mgz |
label/aparc.annot.DKTatlas.ctab |
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?h.white |
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?h.pial |
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?h.thickness |
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-pctsurfcon |
rawavg.mgz |
pctsurfcon --s <subjid> --?h-only |
?h.w-g.pct.mgh |
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orig.mgz |
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?h.cortex.label |
stats/?h.w-g.pct.stats |
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?h.white |
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-hyporelabel |
aseg.presurf.mgz |
mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz |
aseg.presurf.hypos.mgz |
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?h.white |
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aseg.presurf.hypos.mgz |
mri_aparc2aseg --s <subjid> --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt |
aparc+aseg.mgz |
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?h.ribbon.mgz |
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label/?h.aparc.annot |
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ribbon.mgz |
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aseg.presurf.hypos.mgz |
mri_aparc2aseg --s <subjid> --volmask --annot aparc.a2009s --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt |
aparc.a2009s+aseg.mgz |
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?h.ribbon.mgz |
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label/?h.aparc.a2009s.annot |
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ribbon.mgz |
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aseg.presurf.hypos.mgz |
mri_aparc2aseg --s <subjid> --volmask --annot aparc.DKTatlas --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt |
aparc.DKTatlas+aseg.mgz |
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?h.ribbon.mgz |
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label/?h.aparc.DKTatlas.annot |
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ribbon.mgz |
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-apas2aseg |
aparc+aseg.mgz |
apas2aseg --i aparc+aseg.mgz --o aseg.mgz |
aseg.mgz |
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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 --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 |
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?h.orig.nofix, ?h.white, ?h.pial |
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aparc+aseg.mgz |
mri_aparc2aseg --s <subjid> --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz |
wmparc.mgz |
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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/WMParcStatsLUT.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*_exvivo.label label/?h.perirhinal_exvivo.label label/?h.entorhinal_exvivo.label |