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| This table shows the recon-all steps for the current '''dev''' version of FreeSurfer. See ReconAllStableTablev4 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]]. See also the OtherUsefulFlags for other recon-all options. ||<rowbgcolor="#000f80">'''recon-all step''' ||'''Individual Flag''' ||'''Input''' ||'''Command Line''' ||'''Output''' || ||<#00ffe0 style="text-align: left;" |16>'''[[recon-all]] -autorecon1 -subjid <subjid>''' || ||<#00ffe0 style="text-align: left;" |2>-i <invol1> -i <invol2> ||<#000eff>invol1.dcm ||<#000eff>[[mri_convert]] invol1.dcm orig/001.mgz ||<#000eff>orig/001.mgz || ||<#000eff>invol2.dcm ||<#000eff>[[mri_convert]] invol2.dcm orig/002.mgz ||<#000eff>orig/002.mgz || ||<#00ffe0 style="text-align: left;" |4>-[[motioncor]] ||<#000eff>orig/001.mgz ||<#000eff style="text-align: left;" |2>[[mri_motion_correct.fsl]] -o rawavg.mgz -wild orig/001.mgz orig/002.mgz ||<#000eff style="text-align: left;" |2>rawavg.mgz || ||<rowbgcolor="#000eff">orig/002.mgz || ||<rowbgcolor="#000eff">rawavg.mgz ||[[mri_convert]] rawavg.mgz orig.mgz --conform ||orig.mgz || ||<rowbgcolor="#000eff">orig.mgz ||[[mri_add_xform_to_header]] -c transforms/talairach.xfm orig.mgz orig.mgz ||orig.mgz || ||<#00ffe0>-[[nuintensitycor]] ||<#000eff>orig.mgz ||<#000eff>[[mri_nu_correct.mni]] --i orig.mgz --o nu.mgz --n 2 ||<#000eff>nu.mgz || ||<#00ffe0 style="text-align: left;" |4>-[[talairach]] ||<#000eff>nu.mgz ||<#000eff>[[talairach_avi]] --i nu.mgz --xfm transforms/talairach.auto.xfm ||<#000eff>transforms/talairach.auto.xfm || ||<rowbgcolor="#000eff">transforms/talairach.auto.xfm ||cp transforms/talairach.auto.xfm transforms/talairach.xfm ||<#000eff>transforms/talairach.xfm || ||<rowbgcolor="#000eff">transforms/talairach.xfm ||<#000eff>[[talairach_afd]] -T 0.005 -xfm transforms/talairach.xfm ||<#000eff>transforms/talairach.xfm || ||<rowbgcolor="#000eff"> ||awk -f $FREESURFER_HOME/bin/extract_talairach_avi_QA.awk transforms/talairach_avi.log ||<#000eff>transforms/talairach_avi.log || ||<#00ffe0>-[[normalization]] ||<#000eff>nu.mgz ||<#000eff>[[mri_normalize]] -g 1 nu.mgz T1.mgz ||<#000eff>T1.mgz || ||<#00ffe0 style="text-align: left;" |3>-[[skullstrip]] ||<#000eff>nu.mgz ||<#000eff>[[mri_em_register]] -skull nu.mgz $FREESURFER_HOME/average/RB_all_withskull_2007-08-08.gca transforms/talairach_with_skull.lta ||<#000eff>transforms/talairach_with_skull.lta || ||<#000eff>T1.mgz ||<#000eff>[[mri_watershed]] -T1 -brain_atlas $FREESURFER_HOME/average/RB_all_withskull_2007-08-08.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz ||<#000eff>brainmask.auto.mgz || ||<rowbgcolor="#000eff">brainmask.auto.mgz ||cp brainmask.auto.mgz brainmask.mgz ||<#000eff>brainmask.mgz || ||<rowbgcolor="#000eff"> ||<#000eff> ||<#000eff> ||<#000eff> ||<#000eff> || ||<#00ffe0 style="text-align: left;" |68>'''[[recon-all]] -autorecon2 -subjid <subjid>''' || ||<#00ffe0 style="text-align: left;" |2>-[[gcareg]] ||<#000eff>brainmask.mgz ||<#000eff style="text-align: left;" |2>[[mri_em_register]] -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB_all_2007-08-08.gca transforms/talairach.lta ||<#000eff style="text-align: left;" |2>transforms/talairach.lta || ||<rowbgcolor="#000eff">nu.mgz || ||<#00ffe0 style="text-align: left;" |3>-[[canorm]] ||<#000eff>brainmask.mgz ||<#000eff style="text-align: left;" |3>[[mri_ca_normalize]] -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB_all_2007-08-08.gca transforms/talairach.lta norm.mgz ||<#000eff style="text-align: left;" |3>norm.mgz || ||<rowbgcolor="#000eff">nu.mgz || ||<rowbgcolor="#000eff">transforms/talairach.lta || ||<#00ffe0 style="text-align: left;" |3>-[[careg]] ||<#000eff>brainmask.mgz ||<#000eff 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_2007-08-08.gca transforms/talairach.m3z ||<#000eff style="text-align: left;" |3>transforms/talairach.m3z || ||<rowbgcolor="#000eff">transforms/talairach.lta || ||<rowbgcolor="#000eff">norm.mgz || ||<#00ffe0 style="text-align: left;" |3>-[[careginv]] ||<#000eff style="text-align: left;" |3>transforms/talairach.m3z ||<#000eff style="text-align: left;" |3>[[mri_ca_register]] -invert-and-save transforms/talairach.m3z ||<#000eff>transforms/talairach.m3z.inv.x.mgz || ||<rowbgcolor="#000eff">transforms/talairach.m3z.inv.y.mgz || ||<rowbgcolor="#000eff">transforms/talairach.m3z.inv.z.mgz || ||<#00ffe0 style="text-align: left;" |2>-[[rmneck]] ||<#000eff>nu.mgz ||<#000eff style="text-align: left;" |2>[[mri_remove_neck]] -radius 25 nu.mgz transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2007-08-08.gca nu_noneck.mgz ||<#000eff style="text-align: left;" |2>nu_noneck.mgz || ||<rowbgcolor="#000eff">transforms/talairach.m3z || ||<#00ffe0 style="text-align: left;" |2>-[[skull-lta]] ||<#000eff>transforms/talairach.lta ||<#000eff style="text-align: left;" |2>[[mri_em_register]] -skull -t transforms/talairach.lta nu_noneck.mgz $FREESURFER_HOME/average/RB_all_withskull_2007-08-08.gca transforms/talairach_with_skull.lta ||<#000eff style="text-align: left;" |2>transforms/talairach_with_skull.lta || ||<rowbgcolor="#000eff">nu_noneck.mgz || ||<#00ffe0 style="text-align: left;" |4>-[[calabel]] ||<#000eff>norm.mgz ||<#000eff style="text-align: left;" |2>[[mri_ca_label]] -align -nobigventricles norm.mgz transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2007-08-08.gca aseg.auto_noCCseg.mgz ||<#000eff style="text-align: left;" |2>aseg.auto_noCCseg.mgz || ||<rowbgcolor="#000eff">transforms/talairach.m3z || ||<rowbgcolor="#000eff">aseg.auto_noCCseg.mgz ||<#000eff style="text-align: left;" |1>[[mri_cc]] -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz <subjid> ||<#000eff>aseg.auto.mgz || ||<rowbgcolor="#000eff">aseg.auto.mgz ||<#000eff>cp aseg.auto.mgz aseg.mgz ||<#000eff>aseg.mgz || ||<#00ffe0 style="text-align: left;" |3>-[[normalization2]] ||<#000eff>brainmask.mgz ||<#000eff style="text-align: left;" |3>[[mri_normalize]] -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz ||<#000eff style="text-align: left;" |3>brain.mgz || ||<rowbgcolor="#000eff">norm.mgz || ||<rowbgcolor="#000eff">aseg.mgz || ||<#00ffe0 style="text-align: left;" |2>-[[maskbfs]] ||<#000eff>brain.mgz ||<#000eff style="text-align: left;" |2>[[mri_mask]] -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz ||<#000eff style="text-align: left;" |2>brain.finalsurfs.mgz || ||<rowbgcolor="#000eff">brainmask.mgz || ||<#00ffe0 style="text-align: left;" |6>-[[segmentation]] ||<#000eff>brain.mgz ||<#000eff>[[mri_segment]] brain.mgz wm.seg.mgz ||<#000eff>wm.seg.mgz || ||<#000eff>wm.seg.mgz ||<#000eff style="text-align: left;" |3>[[mri_edit_wm_with_aseg]] wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz ||<#000eff style="text-align: left;" |3>wm.asegedit.mgz || ||<rowbgcolor="#000eff">aseg.mgz || ||<rowbgcolor="#000eff">brain.mgz || ||<#000eff>wm.asegedit.mgz ||<#000eff style="text-align: left;" |2>[[mri_pretess]] wm.asegedit.mgz wm norm.mgz wm.mgz ||<#000eff style="text-align: left;" |2>wm.mgz || ||<rowbgcolor="#000eff">norm.mgz || ||<#00ffe0 style="text-align: left;" |3>-[[fill]] ||<#000eff>wm.mgz ||<#000eff style="text-align: left;" |3>[[mri_fill]] -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz ||<#000eff>filled.mgz || ||<rowbgcolor="#000eff">aseg.auto_noCCseg.mgz ||<#000eff style="text-align: left;" |2>../scripts/ponscc.cut.log || ||<rowbgcolor="#000eff">transforms/talairach.lta || ||<#00ffe0 style="text-align: left;" |8>-[[tessellate]] ||<#000eff>filled.mgz ||<#000eff style="text-align: left;" |2>[[mri_pretess]] filled.mgz 255 norm.mgz filled-pretess255.mgz ||<#000eff style="text-align: left;" |2>filled-pretess255.mgz || ||<#000eff>norm.mgz || ||<#000eff>filled-pretess255.mgz ||<#000eff>[[mri_tessellate]] filled-pretess255.mgz 255 lh.orig.nofix ||<#000eff>lh.orig.nofix || ||<#000eff>filled.mgz ||<#000eff style="text-align: left;" |2>[[mri_pretess]] filled.mgz 127 norm.mgz filled-pretess127.mgz ||<#000eff style="text-align: left;" |2>filled-pretess127.mgz || ||<#000eff>norm.mgz || ||<#000eff>filled-pretess127.mgz ||<#000eff>[[mri_tessellate]] filled-pretess127.mgz 127 rh.orig.nofix ||<#000eff>rh.orig.nofix || ||<#000eff>?h.orig.nofix ||<#000eff>[[mris_extract_main_component]] ?h.orig.nofix ?h.orig.nofix ||<#000eff>?h.orig.nofix || ||<#000eff> ||<#000eff>rm -f filled-pretess255.mgz filled-pretess127.mgz ||<#000eff> || ||<#00ffe0>-[[smooth|smooth1]] ||<#000eff>?h.orig.nofix ||<#000eff>[[mris_smooth]] -nw ?h.orig.nofix ?h.smoothwm.nofix ||<#000eff>?h.smoothwm.nofix || ||<#00ffe0>-[[inflate|inflate1]] ||<#000eff>?h.smoothwm.nofix ||<#000eff>[[mris_inflate]] -no-save-sulc ?h.smoothwm.nofix ?h.inflated.nofix ||<#000eff>?h.inflated.nofix || ||<#00ffe0>-[[qsphere]] ||<#000eff>?h.inflated.nofix ||<#000eff>[[mris_sphere]] -q ?h.inflated.nofix ?h.qsphere.nofix ||<#000eff>?h.qsphere.nofix || ||<#00ffe0 style="text-align: left;" |6>-[[fix]] ||<#000eff>?h.orig.nofix ||<#000eff>cp ?h.orig.nofix ?h.orig ||<#000eff>?h.orig || ||<#000eff>?h.inflated.nofix ||<#000eff>cp ?h.inflated.nofix ?h.inflated ||<#000eff>?h.inflated || ||<#000eff>?h.qsphere.nofix ||<#000eff>[[mris_fix_topology]] -mgz -sphere qsphere.nofix -ga <subjid> ?h ||<#000eff>?h.orig || ||<#000eff>?h.orig ||<#000eff>[[mris_euler_number]] ?h.orig ||<#000eff>?h.orig || ||<#000eff>?h.orig ||<#000eff>[[mris_remove_intersection]] ?h.orig ?h.orig ||<#000eff>?h.orig || ||<#000eff> ||<#000eff>rm ?h.inflated ||<#000eff> || ||<#00ffe0 style="text-align: left;" |7>-[[finalsurfs]] ||<#000eff style="text-align: left;" |3>brain.finalsurfs.mgz ||<#000eff style="text-align: left;" |7>[[mris_make_surfaces]] -noaparc -mgz -T1 brain.finalsurfs <subjid> ?h ||<#000eff>?h.white || ||<rowbgcolor="#000eff">?h.pial || ||<rowbgcolor="#000eff">?h.thickness || ||<rowbgcolor="#000eff"style="text-align: left;" |4>?h.orig || ||<rowbgcolor="#000eff">?h.curv || ||<rowbgcolor="#000eff">?h.area || ||<rowbgcolor="#000eff">?h.cortex.label || ||<#00ffe0 style="text-align: left;" |5>-[[surfvolume]] ||<#000eff style="text-align: left;" |1>?h.area ||<#000eff style="text-align: left;" |2>[[mris_calc]] -o ?h.area.mid ?h.area add ?h.area.pial ||<#000eff style="text-align: left;" |2>?h.area.mid || ||<rowbgcolor="#000eff">?h.area.pial || ||<#000eff style="text-align: left;" |1>?h.area.mid ||<#000eff style="text-align: left;" |1>[[mris_calc]] -o ?h.area.mid ?h.area.mid div 2 ||<#000eff>?h.area.mid || ||<#000eff style="text-align: left;" |1>?h.area.mid ||<#000eff style="text-align: left;" |2>[[mris_calc]] -o ?h.volume ?h.area.mid mul ?h.thickness ||<#000eff style="text-align: left;" |2>?h.volume || ||<rowbgcolor="#000eff">?h.thickness || ||<#00ffe0>-[[smooth|smooth2]] ||<#000eff>?h.white ||<#000eff>[[mris_smooth]] -n 3 -nw ?h.white ?h.smoothwm ||<#000eff>?h.smoothwm || ||<#00ffe0 style="text-align: left;" |4>-[[inflate|inflate2]] ||<#000eff style="text-align: left;" |2>?h.smoothwm ||<#000eff style="text-align: left;" |2>[[mris_inflate]] ?h.smoothwm ?h.inflated ||<#000eff>?h.inflated || ||<rowbgcolor="#000eff"style="text-align: left;">?h.sulc || ||<#000eff style="text-align: left;" |2>?h.inflated ||<#000eff style="text-align: left;" |2>[[mris_curvature]] -thresh .999 -n -a 5 -w -distances 10 10 ?h.inflated ||<#000eff>?h.inflated.H || ||<#000eff>?h.inflated.K || ||<rowbgcolor="#000eff"> ||<#000eff> ||<#000eff> ||<#000eff> ||<#000eff> || ||<#00ffe0 style="text-align: left;" |24>'''[[recon-all]] -autorecon3 -subjid <subjid>''' || ||<#00ffe0>-[[sphere]] ||<#000eff>?h.inflated,?h.smoothwm ||<#000eff>[[mris_sphere]] ?h.inflated ?h.sphere ||<#000eff>?h.sphere || ||<#00ffe0>-[[surfreg]] ||<#000eff>?h.sphere ||<#000eff>[[mris_register]] -curv ?h.sphere $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif ?h.sphere.reg ||<#000eff>?h.sphere.reg || ||<#00ffe0 style="text-align: left;" |2>-[[jacobian_white]] ||<#000eff>?h.white ||<#000eff style="text-align: left;" |2>[[mris_jacobian]] ?h.white ?h.sphere.reg ?h.jacobian_white ||<#000eff style="text-align: left;" |2>?h.jacobian_white || ||<rowbgcolor="#000eff">?h.sphere.reg || ||<#00ffe0>-[[avgcurv]] ||<#000eff>?h.sphere.reg ||<#000eff>[[mrisp_paint]] -a 5 $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif#6 ?h.sphere.reg ?h.avg_curv ||<#000eff>?h.avg_curv || ||<#00ffe0 style="text-align: left;" |2>-[[cortparc]] ||<#000eff>aseg.mgz ||<#000eff style="text-align: left;" |2>[[mris_ca_label]] -aseg mri/aseg.mgz <subjid> ?h ?h.sphere.reg $FREESURFER_HOME/average/?h.curvature.buckner40.filled.desikan_killiany.2007-06-20gcs ?h.aparc.annot ||<#000eff style="text-align: left;" |2>label/?h.aparc.annot || ||<rowbgcolor="#000eff">?h.sphere.reg || ||<#00ffe0>-[[parcstats]] ||<#000eff>label/?h.aparc.annot ||<#000eff>[[mris_anatomical_stats]] -mgz -f stats/?h.aparc.stats -b -a label/?h.aparc.annot -c label/aparc.annot.ctab <subjid> ?h ||<#000eff>stats/?h.aparc.stats label/aparc.annot.ctab || ||<#00ffe0 style="text-align: left;" |2>-[[cortparc|cortparc2]] ||<#000eff>aseg.mgz ||<#000eff style="text-align: left;" |2>[[mris_ca_label]] -aseg aseg.mgz <subjid> ?h ?h.sphere.reg $FREESURFER_HOME/average/?h.destrieux.simple.2009-07-29.gcs label/?h.aparc.a2009s.annot ||<#000eff style="text-align: left;" |2>label/?h.aparc.a2009s.annot || ||<rowbgcolor="#000eff">?h.sphere.reg || ||<#00ffe0>-[[parcstats|parcstats2]] ||<#000eff>label/?h.aparc.a2009s.annot ||<#000eff>[[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 ||<#000eff>stats/?h.aparc.a2009s.stats stats/aparc.annot.a2009s.ctab || ||<#00ffe0>-[[segstats]] ||<#000eff>aseg.mgz ||<#000eff>[[mri_segstats]] --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --ctab $FREESURFER_HOME/ASegStatsLUT.txt --subject <subjid> ||<#000eff>stats/aseg.stats || ||<#00ffe0 style="text-align: left;" |3>-[[cortribbon]] ||<#000eff>aseg.mgz ||<#000eff 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> ||<#000eff style="text-align: left;" |3>?h.ribbon.mgz || ||<rowbgcolor="#000eff">?h.white || ||<rowbgcolor="#000eff">?h.pial || ||<#00ffe0 style="text-align: left;" |6>-[[aparc2aseg]] ||<#000eff>aseg.mgz ||<#000eff style="text-align: left;" |3>[[mri_aparc2aseg]] --s <subjid> --ribbon ||<#000eff style="text-align: left;" |3>aparc+aseg.mgz || ||<rowbgcolor="#000eff">?h.ribbon.mgz || ||<rowbgcolor="#000eff">label/?h.aparc.annot || ||<#000eff>aseg.mgz ||<#000eff style="text-align: left;" |3>[[mri_aparc2aseg]] --s <subjid> --ribbon --a2009s ||<#000eff style="text-align: left;" |3>aparc.a2009s+aseg.mgz || ||<rowbgcolor="#000eff">?h.ribbon.mgz || ||<rowbgcolor="#000eff">label/?h.aparc.a2009s.annot || ||<#00ffe0 style="text-align: left;" |2>-[[wmparc]] ||<#000eff>aparc+aseg.mgz ||<#000eff style="text-align: left;" |1>[[mri_aparc2aseg]] --s <subjid> --labelwm --hypo-as-wm --rip-unknown --ribbon --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz ||<#000eff style="text-align: left;" |1>wmparc.mgz || ||<#000eff>wmparc.mgz ||<#000eff style="text-align: left;" |1>[[mri_segstats]] --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject <subjid> --surf-wm-vol --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt ||<#000eff style="text-align: left;" |1>stats/wmparc.stats || ||<rowbgcolor="#000eff"> ||<#000eff> ||<#000eff> ||<#000eff> ||<#000eff> || |
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| ||<rowbgcolor='#80FF80'>'''recon-all step'''||'''Individual Flag'''||'''Input'''||'''Command Line'''||'''Output'''|| ||<bgcolor='#FFFFE0'>none||<bgcolor='#FFFFE0'>none||<bgcolor='#E0E0FF'>file.dcm||<bgcolor='#E0E0FF'>["mri_convert"] file.dcm orig/001.mgz||<bgcolor='#E0E0FF'>orig/001.mgz|| ||<|10(bgcolor='#FFFFE0'>["recon-all"] -autorecon1 -subjid subj|| ||<|3(bgcolor='#FFFFE0'>-motioncor||<bgcolor='#E0E0FF'>orig/001.mgz||<|2(bgcolor='#E0E0FF'>["mri_motion_correct2"] -i orig/001.mgz -i orig/002.mgz -o rawavg.mgz||<|2(bgcolor='#E0E0FF'>rawavg.mgz|| ||<rowbgcolor='#E0E0FF'>orig/002.mgz|| ||<rowbgcolor='#E0E0FF'>rawavg.mgz||["mri_convert"] rawavg.mgz orig.mgz --conform||orig.mgz|| ||<|3(bgcolor='#FFFFE0'>-nuintensitycor||<bgcolor='#E0E0FF'>orig.mgz||<bgcolor='#E0E0FF'>["mri_convert"] orig.mgz nu0.mnc||<bgcolor='#E0E0FF'>nu0.mnc|| ||<rowbgcolor='#E0E0FF'>nu0.mnc||(4 iterations of) ["nu_correct"] -clobber nu0.mnc nu1.mnc||nu4.mnc|| ||<rowbgcolor='#E0E0FF'>nu4.mnc||["mri_convert"] nu4.mnc nu.mgz||nu.mgz|| ||<bgcolor='#FFFFE0'>-talairach||<bgcolor='#E0E0FF'>nu.mgz||<bgcolor='#E0E0FF'>["talairach2"] subjid -mgz||<bgcolor='#E0E0FF'>transforms/talairach.xfm|| ||<bgcolor='#FFFFE0'>-normalization||<bgcolor='#E0E0FF'>nu.mgz||<bgcolor='#E0E0FF'>["mri_normalize"] nu.mgz T1.mgz||<bgcolor='#E0E0FF'>T1.mgz|| ||<bgcolor='#FFFFE0'>-skullstrip||<bgcolor='#E0E0FF'>T1.mgz||<bgcolor='#E0E0FF'>["mri_watershed"] T1.mgz brain.mgz||<bgcolor='#E0E0FF'>brain.mgz|| ||<-5(rowbgcolor='#FF8080'>Check skullstrip (brain.mgz), talairach (transforms/talairach.xfm), and normalization (brain.mgz or T1.mgz - mean wm voxel value = 110)|| ||<|36(bgcolor='#FFFFE0'>["recon-all"] -autorecon2 -subjid subj|| ||<|2(bgcolor='#FFFFE0'>-gcareg||<bgcolor='#E0E0FF'>brain.mgz||<|2(bgcolor='#E0E0FF'>["mri_em_register"] -mask brain.mgz -p .5 -fsamples fsamples.mgz nu.mgz $GCA transforms/talairach.lta||<|2(bgcolor='#E0E0FF'>transforms/talairach.lta|| ||<rowbgcolor='#E0E0FF'>nu.mgz|| ||<|3(bgcolor='#FFFFE0'>-canorm||<bgcolor='#E0E0FF'>brain.mgz||<|3(bgcolor='#E0E0FF'>["mri_ca_normalize"] -mask brain.mgz nu.mgz $GCA transforms/talairach.lta norm.mgz||<|3(bgcolor='#E0E0FF'>norm.mgz|| ||<rowbgcolor='#E0E0FF'>nu.mgz|| ||<rowbgcolor='#E0E0FF'>transforms/talairach.lta|| ||<|3(bgcolor='#FFFFE0'>-careg||<bgcolor='#E0E0FF'>brain.mgz||<|3(bgcolor='#E0E0FF'>["mri_ca_register"] -cross-sequence -mask brain.mgz -T transforms/talairach.lta norm.mgz $GCA transforms/talairach.m3z||<|3(bgcolor='#E0E0FF'>transforms/talairach.m3z|| ||<rowbgcolor='#E0E0FF'>transforms/talairach.lta|| ||<rowbgcolor='#E0E0FF'>norm.mgz|| ||<|2(bgcolor='#FFFFE0'>-calabel||<bgcolor='#E0E0FF'>norm.mgz||<|2(bgcolor='#E0E0FF'>["mri_ca_label"] -cross-sequence norm.mgz transforms/talairach.m3z $GCA aseg.mgz||<|2(bgcolor='#E0E0FF'>aseg.mgz|| ||<rowbgcolor='#E0E0FF'>transforms/talairach.m3z|| ||<bgcolor='#FFFFE0'>-segstats||<bgcolor='#E0E0FF'>aseg.mgz||<bgcolor='#E0E0FF'>["mri_segstats"] --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --in mri/orig.mgz --ctab-default --excludeid 0 --brain-vol-from-seg --brainmask mri/brain.mgz||<bgcolor='#E0E0FF'>stats/aseg.stats|| ||<|4(bgcolor='#FFFFE0'>-normalization2||<bgcolor='#E0E0FF'>brain.mgz||<|2(bgcolor='#E0E0FF'>["mri_normalize"] -mask brain.mgz nu.mgz T1.mgz||<|2(bgcolor='#E0E0FF'>T1.mgz|| ||<rowbgcolor='#E0E0FF'>nu.mgz|| ||<rowbgcolor='#E0E0FF'>T1.mgz||<|2(>["mri_mask"] T1.mgz brain.mgz brain.mgz||<|2(>brain.mgz|| ||<rowbgcolor='#E0E0FF'>brain.mgz|| ||<bgcolor='#FFFFE0'>-segmentation||<bgcolor='#E0E0FF'>brain.mgz||<bgcolor='#E0E0FF'>["mri_segment"] brain.mgz wm.mgz||<bgcolor='#E0E0FF'>wm.mgz|| ||<|2(bgcolor='#FFFFE0'>-edit_wm_with_aseg||<bgcolor='#E0E0FF'>wm.mgz||<|2(bgcolor='#E0E0FF'>["mri_edit_wm_with_aseg"] wm.mgz aseg.mgz wm.mgz||<|2(bgcolor='#E0E0FF'>wm.mgz|| ||<rowbgcolor='#E0E0FF'>aseg.mgz|| ||<|2(bgcolor='#FFFFE0'>-fill||<bgcolor='#E0E0FF'>wm.mgz||<|2(bgcolor='#E0E0FF'>["mri_fill"] -a ../scripts/ponscc.cut.log -xform transforms/talairach.xfm -segmentation aseg.mgz wm.mgz filled.mgz||<bgcolor='#E0E0FF'>filled.mgz|| ||<rowbgcolor='#E0E0FF'>aseg.mgz||../scripts/ponscc.cut.log|| ||<|2((bgcolor='#FFFFE0'>-tessellate||<|2(bgcolor='#E0E0FF'>filled.mgz||<bgcolor='#E0E0FF'>["mri_tessellate"] filled.mgz 255 ../surf/lh.orig||<bgcolor='#E0E0FF'>lh.orig|| ||<rowbgcolor='#E0E0FF'>["mri_tessellate"] filled.mgz 127 ../surf/rh.orig||rh.orig|| ||<bgcolor='#FFFFE0'>-smooth1||<bgcolor='#E0E0FF'>?h.orig||<bgcolor='#E0E0FF'>["mris_smooth"] ?h.orig ?h.smoothwm||<bgcolor='#E0E0FF'>?h.smoothwm|| ||<bgcolor='#FFFFE0'>-inflate1||<bgcolor='#E0E0FF'>?h.smoothwm||<bgcolor='#E0E0FF'>["mris_inflate"] ?h.smoothwm ?h.inflated||<bgcolor='#E0E0FF'>?h.inflated|| ||<bgcolor='#FFFFE0'>-qsphere||<bgcolor='#E0E0FF'>?h.inflated||<bgcolor='#E0E0FF'>["mris_sphere"] -w 0 -inflate -in 200 -q ?h.inflated ?h.qsphere||<bgcolor='#E0E0FF'>?h.qsphere|| ||<bgcolor='#FFFFE0'>-fix||<bgcolor='#E0E0FF'>?h.qsphere||<bgcolor='#E0E0FF'>["mris_fix_topology"] subj ?h||<bgcolor='#E0E0FF'>?h.orig|| ||<bgcolor='#FFFFE0'>-euler||<bgcolor='#E0E0FF'>?h.orig||<bgcolor='#E0E0FF'>["mris_euler_number"] ?h.orig||<bgcolor='#E0E0FF'>?h.orig.euler|| ||<bgcolor='#FFFFE0'>-smooth2||<bgcolor='#E0E0FF'>?h.orig||<bgcolor='#E0E0FF'>["mris_smooth"] ?h.orig ?h.smoothwm||<bgcolor='#E0E0FF'>?h.smoothwm|| ||<bgcolor='#FFFFE0'>-inflate2||<bgcolor='#E0E0FF'>?h.smoothwm||<bgcolor='#E0E0FF'>["mris_inflate"] ?h.smoothwm ?h.inflated||<bgcolor='#E0E0FF'>?h.inflated|| ||<|3(bgcolor='#FFFFE0'>-finalsurfs||<bgcolor='#E0E0FF'>brain.mgz||<|3(bgcolor='#E0E0FF'>["mris_make_surfaces"] -w 0 subj ?h||<bgcolor='#E0E0FF'>?h.white|| ||<|2(rowbgcolor='#E0E0FF'>?h.orig||?h.pial|| ||<rowbgcolor='#E0E0FF'>?h.thickness|| ||<|3(bgcolor='#FFFFE0'>-cortribbon||<bgcolor='#E0E0FF'>orig.mgz||<|3(bgcolor='#E0E0FF'>["mri_surf2vol"] --mkmask --hemi ?h --fillribbon --template orig.mgz --volregidentity subj --outvol ?h.ribbon.mgz||<|3(bgcolor='#E0E0FF'>?h.ribbon.mgz|| ||<rowbgcolor='#E0E0FF'>?h.white|| ||<rowbgcolor='#E0E0FF'>?h.pial|| ||<-5(rowbgcolor='#FF8080'>Check final surfaces '''tkmedit subj wm.mgz ?h.white brain.mgz'''|| ||<|8(bgcolor='#FFFFE0'>["recon-all"] -autorecon3 -subjid subj|| ||<bgcolor='#FFFFE0'>-sphere||<bgcolor='#E0E0FF'>?h.inflated||<bgcolor='#E0E0FF'>["mris_sphere"] -w 0 ?h.inflated ?h.sphere||<bgcolor='#E0E0FF'>?h.sphere|| ||<bgcolor='#FFFFE0'>-surfreg||<bgcolor='#E0E0FF'>?h.sphere||<bgcolor='#E0E0FF'>["mris_register"] -w 0 -curv ?h.sphere $AvgTif ?h.sphere.reg||<bgcolor='#E0E0FF'>?h.sphere.reg|| ||<|2(bgcolor='#FFFFE0'>-contrasurfreg||<bgcolor='#E0E0FF'>rh.sphere||<bgcolor='#E0E0FF'>["mris_register"] -w 0 -curv -reverse rh.sphere $AvgTif rh.lh.sphere.reg||<bgcolor='#E0E0FF'>rh.lh.sphere.reg|| ||<rowbgcolor='#E0E0FF'>lh.sphere||["mris_register"] -w 0 -curv -reverse lh.sphere $AvgTif lh.rh.sphere.reg||lh.rh.sphere.reg|| ||<bgcolor='#FFFFE0'>-avgcurv||<bgcolor='#E0E0FF'>?h.sphere.reg||<bgcolor='#E0E0FF'>["mrisp_paint"] -a 5 $AvgTif#6 ?h.sphere.reg ?h.avg_curv||<bgcolor='#E0E0FF'>?h.avg_curv|| ||<bgcolor='#FFFFE0'>-cortparc||<bgcolor='#E0E0FF'>?h.sphere.reg||<bgcolor='#E0E0FF'>["mris_ca_label"] -t $CPAnnotTable subj ?h sphere.reg $CPAtlas ?h.aparc.annot||<bgcolor='#E0E0FF'>label/?h.aparc.annot|| ||<bgcolor='#FFFFE0'>-parcstats||<bgcolor='#E0E0FF'>label/?h.aparc.annot||<bgcolor='#E0E0FF'>["mris_anatomical_stats"] -f scripts/?h.aparc.stats -b -a label/?h.aparc.annot subj ?h||<bgcolor='#E0E0FF'>stats/?h.aparc.stats|| |
|
| Line 64: | Line 124: |
| Click here to see a table of OtherUsefulFlags | === Differences from Stablev4.0.2 === * mri_cc uses aseg.mgz whereas in v4.0.2, mri_cc uses aseg.auto.mgz. * For those using v4.0.2, this means that if edits are made to the aseg.mgz, you must copy the aseg.mgz to aseg.auto.mgz before running -ccseg to generate a new cc segmentation based on your edits. |
FreeSurfer Tutorial: Process Flow
This table shows the recon-all steps for the current dev version of FreeSurfer. See ReconAllStableTablev4 to see a process flow for the latest stable version of FreeSurfer.
Click here to see this information presented in a block diagram format and here for a process v. files table.
See also the OtherUsefulFlags for other recon-all options.
recon-all step |
Individual Flag |
Input |
Command Line |
Output |
recon-all -autorecon1 -subjid <subjid> |
||||
-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 |
||
orig/001.mgz |
mri_motion_correct.fsl -o rawavg.mgz -wild orig/001.mgz orig/002.mgz |
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 --i orig.mgz --o nu.mgz --n 2 |
nu.mgz |
||
nu.mgz |
talairach_avi --i nu.mgz --xfm transforms/talairach.auto.xfm |
transforms/talairach.auto.xfm |
||
transforms/talairach.auto.xfm |
cp transforms/talairach.auto.xfm transforms/talairach.xfm |
transforms/talairach.xfm |
||
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 |
||
nu.mgz |
mri_normalize -g 1 nu.mgz T1.mgz |
T1.mgz |
||
nu.mgz |
mri_em_register -skull nu.mgz $FREESURFER_HOME/average/RB_all_withskull_2007-08-08.gca transforms/talairach_with_skull.lta |
transforms/talairach_with_skull.lta |
||
T1.mgz |
mri_watershed -T1 -brain_atlas $FREESURFER_HOME/average/RB_all_withskull_2007-08-08.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz |
brainmask.auto.mgz |
||
brainmask.auto.mgz |
cp brainmask.auto.mgz brainmask.mgz |
brainmask.mgz |
||
|
|
|
|
|
recon-all -autorecon2 -subjid <subjid> |
||||
brainmask.mgz |
mri_em_register -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB_all_2007-08-08.gca transforms/talairach.lta |
transforms/talairach.lta |
||
nu.mgz |
||||
brainmask.mgz |
mri_ca_normalize -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB_all_2007-08-08.gca transforms/talairach.lta norm.mgz |
norm.mgz |
||
nu.mgz |
||||
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_2007-08-08.gca transforms/talairach.m3z |
transforms/talairach.m3z |
||
transforms/talairach.lta |
||||
norm.mgz |
||||
transforms/talairach.m3z |
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 |
||||
nu.mgz |
mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2007-08-08.gca nu_noneck.mgz |
nu_noneck.mgz |
||
transforms/talairach.m3z |
||||
transforms/talairach.lta |
mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz $FREESURFER_HOME/average/RB_all_withskull_2007-08-08.gca transforms/talairach_with_skull.lta |
transforms/talairach_with_skull.lta |
||
nu_noneck.mgz |
||||
norm.mgz |
mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2007-08-08.gca aseg.auto_noCCseg.mgz |
aseg.auto_noCCseg.mgz |
||
transforms/talairach.m3z |
||||
aseg.auto_noCCseg.mgz |
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 |
||
brainmask.mgz |
mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz |
brain.mgz |
||
norm.mgz |
||||
aseg.mgz |
||||
brain.mgz |
mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz |
brain.finalsurfs.mgz |
||
brainmask.mgz |
||||
brain.mgz |
mri_segment brain.mgz wm.seg.mgz |
wm.seg.mgz |
||
wm.seg.mgz |
mri_edit_wm_with_aseg wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz |
wm.asegedit.mgz |
||
aseg.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 |
|
||
brain.finalsurfs.mgz |
mris_make_surfaces -noaparc -mgz -T1 brain.finalsurfs <subjid> ?h |
?h.white |
||
?h.pial |
||||
?h.thickness |
||||
?h.orig |
||||
?h.curv |
||||
?h.area |
||||
?h.cortex.label |
||||
?h.area |
mris_calc -o ?h.area.mid ?h.area add ?h.area.pial |
?h.area.mid |
||
?h.area.pial |
||||
?h.area.mid |
mris_calc -o ?h.area.mid ?h.area.mid div 2 |
?h.area.mid |
||
?h.area.mid |
mris_calc -o ?h.volume ?h.area.mid mul ?h.thickness |
?h.volume |
||
?h.thickness |
||||
?h.white |
mris_smooth -n 3 -nw ?h.white ?h.smoothwm |
?h.smoothwm |
||
?h.smoothwm |
mris_inflate ?h.smoothwm ?h.inflated |
?h.inflated |
||
?h.sulc |
||||
?h.inflated |
mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ?h.inflated |
?h.inflated.H |
||
?h.inflated.K |
||||
|
|
|
|
|
recon-all -autorecon3 -subjid <subjid> |
||||
?h.inflated,?h.smoothwm |
mris_sphere ?h.inflated ?h.sphere |
?h.sphere |
||
?h.sphere |
mris_register -curv ?h.sphere $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif ?h.sphere.reg |
?h.sphere.reg |
||
?h.white |
mris_jacobian ?h.white ?h.sphere.reg ?h.jacobian_white |
?h.jacobian_white |
||
?h.sphere.reg |
||||
?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 |
||
aseg.mgz |
mris_ca_label -aseg mri/aseg.mgz <subjid> ?h ?h.sphere.reg $FREESURFER_HOME/average/?h.curvature.buckner40.filled.desikan_killiany.2007-06-20gcs ?h.aparc.annot |
label/?h.aparc.annot |
||
?h.sphere.reg |
||||
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 |
||
aseg.mgz |
mris_ca_label -aseg aseg.mgz <subjid> ?h ?h.sphere.reg $FREESURFER_HOME/average/?h.destrieux.simple.2009-07-29.gcs label/?h.aparc.a2009s.annot |
label/?h.aparc.a2009s.annot |
||
?h.sphere.reg |
||||
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 |
||
aseg.mgz |
mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --ctab $FREESURFER_HOME/ASegStatsLUT.txt --subject <subjid> |
stats/aseg.stats |
||
aseg.mgz |
mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance <subjid> |
?h.ribbon.mgz |
||
?h.white |
||||
?h.pial |
||||
aseg.mgz |
mri_aparc2aseg --s <subjid> --ribbon |
aparc+aseg.mgz |
||
?h.ribbon.mgz |
||||
label/?h.aparc.annot |
||||
aseg.mgz |
mri_aparc2aseg --s <subjid> --ribbon --a2009s |
aparc.a2009s+aseg.mgz |
||
?h.ribbon.mgz |
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label/?h.aparc.a2009s.annot |
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aparc+aseg.mgz |
mri_aparc2aseg --s <subjid> --labelwm --hypo-as-wm --rip-unknown --ribbon --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz |
wmparc.mgz |
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wmparc.mgz |
mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject <subjid> --surf-wm-vol --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt |
stats/wmparc.stats |
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Differences from Stablev4.0.2
- mri_cc uses aseg.mgz whereas in v4.0.2, mri_cc uses aseg.auto.mgz.
- For those using v4.0.2, this means that if edits are made to the aseg.mgz, you must copy the aseg.mgz to aseg.auto.mgz before running -ccseg to generate a new cc segmentation based on your edits.