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| '''This table shows the recon-all steps for the current ''dev'' version of FreeSurfer.''' See ReconAllStableTablev4 for the latest ''stable'' version of FreeSurfer. Click [wiki:Self:ReconAllBlockDiagram here] to see this information presented in a block diagram format and [wiki:Self:ReconAllFilesVsSteps here for a process v. files table]. See also the OtherUsefulFlags for other recon-all options. ||<rowbgcolor='#80FF80'>'''recon-all step'''||'''Individual Flag'''||'''Input'''||'''Command Line'''||'''Output'''|| ||<|16(bgcolor='#FFFFE0'>'''["recon-all"] -autorecon1 -subjid <subjid>'''|| ||<|2(bgcolor='#FFFFE0'>-i <invol1> -i <invol2>||<bgcolor='#E0E0FF'>invol1.dcm||<bgcolor='#E0E0FF'>["mri_convert"] invol1.dcm orig/001.mgz||<bgcolor='#E0E0FF'>orig/001.mgz|| ||<bgcolor='#E0E0FF'>invol2.dcm||<bgcolor='#E0E0FF'>["mri_convert"] invol2.dcm orig/002.mgz||<bgcolor='#E0E0FF'>orig/002.mgz|| ||<|4(bgcolor='#FFFFE0'>-motioncor||<bgcolor='#E0E0FF'>orig/001.mgz||<|2(bgcolor='#E0E0FF'>["mri_motion_correct.fsl"] -o rawavg.mgz -wild orig/001.mgz orig/002.mgz ||<|2(bgcolor='#E0E0FF'>rawavg.mgz|| ||<rowbgcolor='#E0E0FF'>orig/002.mgz|| ||<rowbgcolor='#E0E0FF'>rawavg.mgz||["mri_convert"] rawavg.mgz orig.mgz --conform||orig.mgz|| ||<rowbgcolor='#E0E0FF'>orig.mgz||["mri_add_xform_to_header"] -c transforms/talairach.xfm orig.mgz orig.mgz||orig.mgz|| ||<bgcolor='#FFFFE0'>-nuintensitycor||<bgcolor='#E0E0FF'>orig.mgz||<bgcolor='#E0E0FF'>["mri_nu_correct.mni"] --i orig.mgz --o nu.mgz --n 2||<bgcolor='#E0E0FF'>nu.mgz|| ||<|4(bgcolor='#FFFFE0'>-talairach||<bgcolor='#E0E0FF'>nu.mgz||<bgcolor='#E0E0FF'>["talairach_avi"] --i nu.mgz --xfm transforms/talairach.auto.xfm||<bgcolor='#E0E0FF'>transforms/talairach.auto.xfm|| ||<rowbgcolor='#E0E0FF'>transforms/talairach.auto.xfm||cp transforms/talairach.auto.xfm transforms/talairach.xfm||<bgcolor='#E0E0FF'>transforms/talairach.xfm|| ||<rowbgcolor='#E0E0FF'>transforms/talairach.xfm||<bgcolor='#E0E0FF'>["talairach_afd"] -T 0.005 -xfm transforms/talairach.xfm||<bgcolor='#E0E0FF'>transforms/talairach.xfm|| ||<rowbgcolor='#E0E0FF'>||awk -f $FREESURFER_HOME/bin/extract_talairach_avi_QA.awk transforms/talairach_avi.log||<bgcolor='#E0E0FF'>transforms/talairach_avi.log|| ||<bgcolor='#FFFFE0'>-normalization||<bgcolor='#E0E0FF'>nu.mgz||<bgcolor='#E0E0FF'>["mri_normalize"] -g 1 nu.mgz T1.mgz||<bgcolor='#E0E0FF'>T1.mgz|| ||<|3(bgcolor='#FFFFE0'>-skullstrip||<bgcolor='#E0E0FF'>nu.mgz||<bgcolor='#E0E0FF'>["mri_em_register"] -skull nu.mgz $FREESURFER_HOME/average/RB_all_withskull_2007-08-08.gca transforms/talairach_with_skull.lta||<bgcolor='#E0E0FF'>transforms/talairach_with_skull.lta|| ||<bgcolor='#E0E0FF'>T1.mgz||<bgcolor='#E0E0FF'>["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||<bgcolor='#E0E0FF'>brainmask.auto.mgz|| ||<rowbgcolor='#E0E0FF'>brainmask.auto.mgz||cp brainmask.auto.mgz brainmask.mgz||<bgcolor='#E0E0FF'>brainmask.mgz|| ||<rowbgcolor='#E0E0FF'>||<bgcolor='#E0E0FF'>||<bgcolor='#E0E0FF'>||<bgcolor='#E0E0FF'>||<bgcolor='#E0E0FF'>|| ||<|73(bgcolor='#FFFFE0'>'''["recon-all"] -autorecon2 -subjid <subjid>'''|| ||<|2(bgcolor='#FFFFE0'>-gcareg||<bgcolor='#E0E0FF'>brainmask.mgz||<|2(bgcolor='#E0E0FF'>["mri_em_register"] -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB_all_2007-08-08.gca transforms/talairach.lta||<|2(bgcolor='#E0E0FF'>transforms/talairach.lta|| ||<rowbgcolor='#E0E0FF'>nu.mgz|| ||<|3(bgcolor='#FFFFE0'>-canorm||<bgcolor='#E0E0FF'>brainmask.mgz||<|3(bgcolor='#E0E0FF'>["mri_ca_normalize"] -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB_all_2007-08-08.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'>brainmask.mgz||<|3(bgcolor='#E0E0FF'>["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||<|3(bgcolor='#E0E0FF'>transforms/talairach.m3z|| ||<rowbgcolor='#E0E0FF'>transforms/talairach.lta|| ||<rowbgcolor='#E0E0FF'>norm.mgz|| ||<|3(bgcolor='#FFFFE0'>-careginv||<|3(bgcolor='#E0E0FF'>transforms/talairach.m3z||<|3(bgcolor='#E0E0FF'>["mri_ca_register"] -invert-and-save transforms/talairach.m3z||<bgcolor='#E0E0FF'>transforms/talairach.m3z.inv.x.mgz|| ||<rowbgcolor='#E0E0FF'>transforms/talairach.m3z.inv.y.mgz|| ||<rowbgcolor='#E0E0FF'>transforms/talairach.m3z.inv.z.mgz|| ||<|2(bgcolor='#FFFFE0'>-rmneck||<bgcolor='#E0E0FF'>nu.mgz||<|2(bgcolor='#E0E0FF'>["mri_remove_neck"] -radius 25 nu.mgz transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2007-08-08.gca nu_noneck.mgz||<|2(bgcolor='#E0E0FF'>nu_noneck.mgz|| ||<rowbgcolor='#E0E0FF'>transforms/talairach.m3z|| ||<|2(bgcolor='#FFFFE0'>-skull-lta||<bgcolor='#E0E0FF'>transforms/talairach.lta||<|2(bgcolor='#E0E0FF'>["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||<|2(bgcolor='#E0E0FF'>transforms/talairach_with_skull.lta|| ||<rowbgcolor='#E0E0FF'>nu_noneck.mgz|| ||<|3(bgcolor='#FFFFE0'>-calabel||<bgcolor='#E0E0FF'>norm.mgz||<|2(bgcolor='#E0E0FF'>["mri_ca_label"] -align -nobigventricles norm.mgz transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2007-08-08.gca aseg.auto.mgz||<|2(bgcolor='#E0E0FF'>aseg.auto.mgz|| ||<rowbgcolor='#E0E0FF'>transforms/talairach.m3z|| ||<rowbgcolor='#E0E0FF'>aseg.auto.mgz||<bgcolor='#E0E0FF'>cp aseg.auto.mgz aseg.mgz||<bgcolor='#E0E0FF'>aseg.mgz|| ||<|2(bgcolor='#FFFFE0'>-ccseg||<bgcolor='#E0E0FF'>aseg.mgz||<|1(bgcolor='#E0E0FF'>["mri_cc"] -aseg aseg.mgz -o aseg.auto_CCseg.mgz <subjid>||<bgcolor='#E0E0FF'>aseg.auto_CCseg.mgz|| ||<rowbgcolor='#E0E0FF'>aseg.auto_CCseg.mgz||<bgcolor='#E0E0FF'>cp aseg.auto_CCseg.mgz aseg.mgz||<bgcolor='#E0E0FF'>aseg.mgz|| ||<|3(bgcolor='#FFFFE0'>-normalization2||<bgcolor='#E0E0FF'>brainmask.mgz||<|3(bgcolor='#E0E0FF'>["mri_normalize"] -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz||<|3(bgcolor='#E0E0FF'>brain.mgz|| ||<rowbgcolor='#E0E0FF'>norm.mgz|| ||<rowbgcolor='#E0E0FF'>aseg.mgz|| ||<|2(bgcolor='#FFFFE0'>-maskbfs||<bgcolor='#E0E0FF'>brain.mgz||<|2(bgcolor='#E0E0FF'>["mri_mask"] -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz||<|2(bgcolor='#E0E0FF'>brain.finalsurfs.mgz|| ||<rowbgcolor='#E0E0FF'>brainmask.mgz|| ||<|6(bgcolor='#FFFFE0'>-segmentation||<bgcolor='#E0E0FF'>brain.mgz||<bgcolor='#E0E0FF'>["mri_segment"] brain.mgz wm.seg.mgz||<bgcolor='#E0E0FF'>wm.seg.mgz|| ||<bgcolor='#E0E0FF'>wm.seg.mgz||<|3(bgcolor='#E0E0FF'>["mri_edit_wm_with_aseg"] wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz||<|3(bgcolor='#E0E0FF'>wm.asegedit.mgz|| ||<rowbgcolor='#E0E0FF'>aseg.mgz|| ||<rowbgcolor='#E0E0FF'>brain.mgz|| ||<bgcolor='#E0E0FF'>wm.asegedit.mgz||<|2(bgcolor='#E0E0FF'>["mri_pretess"] wm.asegedit.mgz wm norm.mgz wm.mgz||<|2(bgcolor='#E0E0FF'>wm.mgz|| ||<rowbgcolor='#E0E0FF'>norm.mgz|| ||<|3(bgcolor='#FFFFE0'>-fill||<bgcolor='#E0E0FF'>wm.mgz||<|3(bgcolor='#E0E0FF'>["mri_fill"] -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto.mgz wm.mgz filled.mgz||<bgcolor='#E0E0FF'>filled.mgz|| ||<rowbgcolor='#E0E0FF'>aseg.mgz||<|2(bgcolor='#E0E0FF'>../scripts/ponscc.cut.log|| ||<rowbgcolor='#E0E0FF'>transforms/talairach.lta|| ||<|8((bgcolor='#FFFFE0'>-tessellate||<bgcolor='#E0E0FF'>filled.mgz||<|2(bgcolor='#E0E0FF'>["mri_pretess"] filled.mgz 255 norm.mgz filled-pretess255.mgz||<|2(bgcolor='#E0E0FF'>filled-pretess255.mgz|| ||<bgcolor='#E0E0FF'>norm.mgz|| ||<bgcolor='#E0E0FF'>filled-pretess255.mgz||<bgcolor='#E0E0FF'>["mri_tessellate"] filled-pretess255.mgz 255 lh.orig.nofix||<bgcolor='#E0E0FF'>lh.orig.nofix|| ||<bgcolor='#E0E0FF'>filled.mgz||<|2(bgcolor='#E0E0FF'>["mri_pretess"] filled.mgz 127 norm.mgz filled-pretess127.mgz||<|2(bgcolor='#E0E0FF'>filled-pretess127.mgz|| ||<bgcolor='#E0E0FF'>norm.mgz|| ||<bgcolor='#E0E0FF'>filled-pretess127.mgz||<bgcolor='#E0E0FF'>["mri_tessellate"] filled-pretess127.mgz 127 rh.orig.nofix||<bgcolor='#E0E0FF'>rh.orig.nofix|| ||<bgcolor='#E0E0FF'>?h.orig.nofix||<bgcolor='#E0E0FF'>["mris_extract_main_component"] ?h.orig.nofix ?h.orig.nofix||<bgcolor='#E0E0FF'>?h.orig.nofix|| ||<bgcolor='#E0E0FF'>||<bgcolor='#E0E0FF'>rm -f filled-pretess255.mgz filled-pretess127.mgz||<bgcolor='#E0E0FF'>|| ||<bgcolor='#FFFFE0'>-smooth1||<bgcolor='#E0E0FF'>?h.orig.nofix||<bgcolor='#E0E0FF'>["mris_smooth"] -nw ?h.orig.nofix ?h.smoothwm.nofix||<bgcolor='#E0E0FF'>?h.smoothwm.nofix|| ||<bgcolor='#FFFFE0'>-inflate1||<bgcolor='#E0E0FF'>?h.smoothwm.nofix||<bgcolor='#E0E0FF'>["mris_inflate"] -no-save-sulc ?h.smoothwm.nofix ?h.inflated.nofix||<bgcolor='#E0E0FF'>?h.inflated.nofix|| ||<bgcolor='#FFFFE0'>-qsphere||<bgcolor='#E0E0FF'>?h.inflated.nofix||<bgcolor='#E0E0FF'>["mris_sphere"] -q ?h.inflated.nofix ?h.qsphere.nofix||<bgcolor='#E0E0FF'>?h.qsphere.nofix|| ||<|6(bgcolor='#FFFFE0'>-fix||<bgcolor='#E0E0FF'>?h.orig.nofix||<bgcolor='#E0E0FF'>cp ?h.orig.nofix ?h.orig||<bgcolor='#E0E0FF'>?h.orig|| ||<bgcolor='#E0E0FF'>?h.inflated.nofix||<bgcolor='#E0E0FF'>cp ?h.inflated.nofix ?h.inflated||<bgcolor='#E0E0FF'>?h.inflated|| ||<bgcolor='#E0E0FF'>?h.qsphere.nofix||<bgcolor='#E0E0FF'>["mris_fix_topology"] -mgz -sphere qsphere.nofix -ga <subjid> ?h||<bgcolor='#E0E0FF'>?h.orig|| ||<bgcolor='#E0E0FF'>?h.orig||<bgcolor='#E0E0FF'>["mris_euler_number"] ?h.orig||<bgcolor='#E0E0FF'>?h.orig|| ||<bgcolor='#E0E0FF'>?h.orig||<bgcolor='#E0E0FF'>["mris_remove_intersection"] ?h.orig ?h.orig||<bgcolor='#E0E0FF'>?h.orig|| ||<bgcolor='#E0E0FF'>||<bgcolor='#E0E0FF'>rm ?h.inflated||<bgcolor='#E0E0FF'>|| ||<|7(bgcolor='#FFFFE0'>-finalsurfs||<|3(bgcolor='#E0E0FF'>brain.finalsurfs.mgz||<|7(bgcolor='#E0E0FF'>["mris_make_surfaces"] -noaparc -mgz -T1 brain.finalsurfs <subjid> ?h||<bgcolor='#E0E0FF'>?h.white|| ||<rowbgcolor='#E0E0FF'>?h.pial|| ||<rowbgcolor='#E0E0FF'>?h.thickness|| ||<|4(rowbgcolor='#E0E0FF'>?h.orig|| ||<rowbgcolor='#E0E0FF'>?h.curv|| ||<rowbgcolor='#E0E0FF'>?h.area|| ||<rowbgcolor='#E0E0FF'>?h.cortex.label|| ||<|5(bgcolor='#FFFFE0'>-surfvolume||<|1(bgcolor='#E0E0FF'>?h.area||<|2(bgcolor='#E0E0FF'>["mris_calc"] -o ?h.area.mid ?h.area add ?h.area.pial||<|2(bgcolor='#E0E0FF'>?h.area.mid|| ||<rowbgcolor='#E0E0FF'>?h.area.pial|| ||<|1(bgcolor='#E0E0FF'>?h.area.mid||<|1(bgcolor='#E0E0FF'>["mris_calc"] -o ?h.area.mid ?h.area.mid div 2||<bgcolor='#E0E0FF'>?h.area.mid|| ||<|1(bgcolor='#E0E0FF'>?h.area.mid||<|2(bgcolor='#E0E0FF'>["mris_calc"] -o ?h.volume ?h.area.mid mul lh.thickness||<|2(bgcolor='#E0E0FF'>?h.volume|| ||<rowbgcolor='#E0E0FF'>?h.volume|| ||<bgcolor='#FFFFE0'>-smooth2||<bgcolor='#E0E0FF'>?h.white||<bgcolor='#E0E0FF'>["mris_smooth"] -n 3 -nw ?h.white ?h.smoothwm||<bgcolor='#E0E0FF'>?h.smoothwm|| ||<|4(bgcolor='#FFFFE0'>-inflate2||<|2(bgcolor='#E0E0FF'>?h.smoothwm||<|2(bgcolor='#E0E0FF'>["mris_inflate"] ?h.smoothwm ?h.inflated||<bgcolor='#E0E0FF'>?h.inflated|| ||<(rowbgcolor='#E0E0FF'>?h.sulc|| ||<|2(bgcolor='#E0E0FF'>?h.inflated||<|2(bgcolor='#E0E0FF'>["mris_curvature"] -thresh .999 -n -a 5 -w -distances 10 10 ?h.inflated||<bgcolor='#E0E0FF'>?h.inflated.H|| ||<bgcolor='#E0E0FF'>?h.inflated.K|| ||<bgcolor='#FFFFE0'>-segstats||<bgcolor='#E0E0FF'>aseg.mgz||<bgcolor='#E0E0FF'>["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>||<bgcolor='#E0E0FF'>stats/aseg.stats|| ||<|3(bgcolor='#FFFFE0'>-cortribbon||<bgcolor='#E0E0FF'>orig.mgz||<|3(bgcolor='#E0E0FF'>["mris_volmask"] --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance <subjid>||<|3(bgcolor='#E0E0FF'>?h.ribbon.mgz|| ||<rowbgcolor='#E0E0FF'>?h.white|| ||<rowbgcolor='#E0E0FF'>?h.pial|| ||<rowbgcolor='#E0E0FF'>||<bgcolor='#E0E0FF'>||<bgcolor='#E0E0FF'>||<bgcolor='#E0E0FF'>||<bgcolor='#E0E0FF'>|| ||<|21(bgcolor='#FFFFE0'>'''["recon-all"] -autorecon3 -subjid <subjid>'''|| ||<bgcolor='#FFFFE0'>-sphere||<bgcolor='#E0E0FF'>?h.inflated||<bgcolor='#E0E0FF'>["mris_sphere"] ?h.inflated ?h.sphere||<bgcolor='#E0E0FF'>?h.sphere|| ||<bgcolor='#FFFFE0'>-surfreg||<bgcolor='#E0E0FF'>?h.sphere||<bgcolor='#E0E0FF'>["mris_register"] -curv ?h.sphere $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif ?h.sphere.reg||<bgcolor='#E0E0FF'>?h.sphere.reg|| ||<|2(bgcolor='#FFFFE0'>-jacobian_white||<bgcolor='#E0E0FF'>?h.white||<|2(bgcolor='#E0E0FF'>["mris_jacobian"] ?h.white ?h.sphere.reg ?h.jacobian_white||<|2(bgcolor='#E0E0FF'>?h.jacobian_white|| ||<rowbgcolor='#E0E0FF'>?h.sphere.reg|| ||<bgcolor='#FFFFE0'>-avgcurv||<bgcolor='#E0E0FF'>?h.sphere.reg||<bgcolor='#E0E0FF'>["mrisp_paint"] -a 5 $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif#6 ?h.sphere.reg ?h.avg_curv||<bgcolor='#E0E0FF'>?h.avg_curv|| ||<|2(bgcolor='#FFFFE0'>-cortparc||<bgcolor='#E0E0FF'>aseg.mgz||<|2(bgcolor='#E0E0FF'>["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||<|2(bgcolor='#E0E0FF'>label/?h.aparc.annot|| ||<rowbgcolor='#E0E0FF'>?h.sphere.reg|| ||<bgcolor='#FFFFE0'>-parcstats||<bgcolor='#E0E0FF'>label/?h.aparc.annot||<bgcolor='#E0E0FF'>["mris_anatomical_stats"] -mgz -f stats/?h.aparc.stats -b -a label/?h.aparc.annot -c label/aparc.annot.ctab <subjid> ?h||<bgcolor='#E0E0FF'>stats/?h.aparc.stats label/aparc.annot.ctab|| ||<|2(bgcolor='#FFFFE0'>-cortparc2||<bgcolor='#E0E0FF'>aseg.mgz||<|2(bgcolor='#E0E0FF'>["mris_ca_label"] -aseg aseg.mgz <subjid> ?h ?h.sphere.reg $FREESURFER_HOME/average/?h.atlas2005_simple.gcs label/?h.aparc.a2005s.annot||<|2(bgcolor='#E0E0FF'>label/?h.aparc.a2005s.annot|| ||<rowbgcolor='#E0E0FF'>?h.sphere.reg|| ||<bgcolor='#FFFFE0'>-parcstats2||<bgcolor='#E0E0FF'>label/?h.aparc.a2005s.annot||<bgcolor='#E0E0FF'>["mris_anatomical_stats"] -mgz -f stats/?h.aparc.a2005s.stats -b -a label/?h.aparc.a2005s.annot -c label/aparc.annot.a2005s.ctab <subjid> ?h||<bgcolor='#E0E0FF'>stats/?h.aparc.a2005s.stats stats/aparc.annot.a2005s.ctab|| ||<|6(bgcolor='#FFFFE0'>-aparc2aseg||<bgcolor='#E0E0FF'> aseg.mgz ||<|3(bgcolor='#E0E0FF'>["mri_aparc2aseg"] --s <subjid> --ribbon||<|3(bgcolor='#E0E0FF'> aparc+aseg.mgz|| ||<rowbgcolor='#E0E0FF'>?h.ribbon.mgz|| ||<rowbgcolor='#E0E0FF'>label/?h.aparc.annot|| ||<bgcolor='#E0E0FF'> aseg.mgz ||<|3(bgcolor='#E0E0FF'>["mri_aparc2aseg"] --s <subjid> --ribbon --a2005s||<|3(bgcolor='#E0E0FF'> aparc.a2005s+aseg.mgz|| ||<rowbgcolor='#E0E0FF'>?h.ribbon.mgz|| ||<rowbgcolor='#E0E0FF'>label/?h.aparc.a2005s.annot|| ||<|3(bgcolor='#FFFFE0'>-wmparc||<bgcolor='#E0E0FF'> aparc+aseg.mgz ||<|1(bgcolor='#E0E0FF'>["mri_aparc2aseg"] --s <subjid> --labelwm --hypo-as-wm --rip-unknown --ribbon --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz||<|1(bgcolor='#E0E0FF'> wmparc.mgz|| ||<bgcolor='#E0E0FF'> wmparc.mgz ||<|1(bgcolor='#E0E0FF'>["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||<|1(bgcolor='#E0E0FF'> wmparc.stats|| |
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| Line 4: | Line 124: |
| ||<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|| 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 for the latest stable version of FreeSurfer.
Click [wiki:ReconAllBlockDiagram here] to see this information presented in a block diagram format and [wiki:ReconAllFilesVsSteps 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 |
||
-motioncor |
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 |
||
-nuintensitycor |
orig.mgz |
["mri_nu_correct.mni"] --i orig.mgz --o nu.mgz --n 2 |
nu.mgz |
|
-talairach |
nu.mgz |
["talairach_avi"] --i nu.mgz --xfm transforms/talairach.auto.xfm |
transforms/talairach.auto.xfm |
|
transforms/talairach.auto.xfm |
cp transforms/talairach.auto.xfm transforms/talairach.xfm |
transforms/talairach.xfm |
||
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 |
nu.mgz |
["mri_normalize"] -g 1 nu.mgz T1.mgz |
T1.mgz |
|
-skullstrip |
nu.mgz |
["mri_em_register"] -skull nu.mgz $FREESURFER_HOME/average/RB_all_withskull_2007-08-08.gca transforms/talairach_with_skull.lta |
transforms/talairach_with_skull.lta |
|
T1.mgz |
["mri_watershed"] -T1 -brain_atlas $FREESURFER_HOME/average/RB_all_withskull_2007-08-08.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz |
brainmask.auto.mgz |
||
brainmask.auto.mgz |
cp brainmask.auto.mgz brainmask.mgz |
brainmask.mgz |
||
["recon-all"] -autorecon2 -subjid <subjid> |
||||
-gcareg |
brainmask.mgz |
["mri_em_register"] -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB_all_2007-08-08.gca transforms/talairach.lta |
transforms/talairach.lta |
|
nu.mgz |
||||
-canorm |
brainmask.mgz |
["mri_ca_normalize"] -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB_all_2007-08-08.gca transforms/talairach.lta norm.mgz |
norm.mgz |
|
nu.mgz |
||||
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_2007-08-08.gca transforms/talairach.m3z |
transforms/talairach.m3z |
|
transforms/talairach.lta |
||||
norm.mgz |
||||
-careginv |
transforms/talairach.m3z |
["mri_ca_register"] -invert-and-save transforms/talairach.m3z |
transforms/talairach.m3z.inv.x.mgz |
|
transforms/talairach.m3z.inv.y.mgz |
||||
transforms/talairach.m3z.inv.z.mgz |
||||
-rmneck |
nu.mgz |
["mri_remove_neck"] -radius 25 nu.mgz transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2007-08-08.gca nu_noneck.mgz |
nu_noneck.mgz |
|
transforms/talairach.m3z |
||||
-skull-lta |
transforms/talairach.lta |
["mri_em_register"] -skull -t transforms/talairach.lta nu_noneck.mgz $FREESURFER_HOME/average/RB_all_withskull_2007-08-08.gca transforms/talairach_with_skull.lta |
transforms/talairach_with_skull.lta |
|
nu_noneck.mgz |
||||
-calabel |
norm.mgz |
["mri_ca_label"] -align -nobigventricles norm.mgz transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2007-08-08.gca aseg.auto.mgz |
aseg.auto.mgz |
|
transforms/talairach.m3z |
||||
aseg.auto.mgz |
cp aseg.auto.mgz aseg.mgz |
aseg.mgz |
||
-ccseg |
aseg.mgz |
["mri_cc"] -aseg aseg.mgz -o aseg.auto_CCseg.mgz <subjid> |
aseg.auto_CCseg.mgz |
|
aseg.auto_CCseg.mgz |
cp aseg.auto_CCseg.mgz aseg.mgz |
aseg.mgz |
||
-normalization2 |
brainmask.mgz |
["mri_normalize"] -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz |
brain.mgz |
|
norm.mgz |
||||
aseg.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"] 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.mgz wm.mgz filled.mgz |
filled.mgz |
|
aseg.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 |
||||
-finalsurfs |
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 |
||||
-surfvolume |
?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 lh.thickness |
?h.volume |
||
?h.volume |
||||
-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 |
||||
?h.inflated |
["mris_curvature"] -thresh .999 -n -a 5 -w -distances 10 10 ?h.inflated |
?h.inflated.H |
||
?h.inflated.K |
||||
-segstats |
aseg.mgz |
["mri_segstats"] --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --ctab $FREESURFER_HOME/ASegStatsLUT.txt --subject <subjid> |
stats/aseg.stats |
|
-cortribbon |
orig.mgz |
["mris_volmask"] --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance <subjid> |
?h.ribbon.mgz |
|
?h.white |
||||
?h.pial |
||||
["recon-all"] -autorecon3 -subjid <subjid> |
||||
-sphere |
?h.inflated |
["mris_sphere"] ?h.inflated ?h.sphere |
?h.sphere |
|
-surfreg |
?h.sphere |
["mris_register"] -curv ?h.sphere $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif ?h.sphere.reg |
?h.sphere.reg |
|
-jacobian_white |
?h.white |
["mris_jacobian"] ?h.white ?h.sphere.reg ?h.jacobian_white |
?h.jacobian_white |
|
?h.sphere.reg |
||||
-avgcurv |
?h.sphere.reg |
["mrisp_paint"] -a 5 $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif#6 ?h.sphere.reg ?h.avg_curv |
?h.avg_curv |
|
-cortparc |
aseg.mgz |
["mris_ca_label"] -aseg mri/aseg.mgz <subjid> ?h ?h.sphere.reg $FREESURFER_HOME/average/?h.curvature.buckner40.filled.desikan_killiany.2007-06-20gcs ?h.aparc.annot |
label/?h.aparc.annot |
|
?h.sphere.reg |
||||
-parcstats |
label/?h.aparc.annot |
["mris_anatomical_stats"] -mgz -f stats/?h.aparc.stats -b -a label/?h.aparc.annot -c label/aparc.annot.ctab <subjid> ?h |
stats/?h.aparc.stats label/aparc.annot.ctab |
|
-cortparc2 |
aseg.mgz |
["mris_ca_label"] -aseg aseg.mgz <subjid> ?h ?h.sphere.reg $FREESURFER_HOME/average/?h.atlas2005_simple.gcs label/?h.aparc.a2005s.annot |
label/?h.aparc.a2005s.annot |
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?h.sphere.reg |
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-parcstats2 |
label/?h.aparc.a2005s.annot |
["mris_anatomical_stats"] -mgz -f stats/?h.aparc.a2005s.stats -b -a label/?h.aparc.a2005s.annot -c label/aparc.annot.a2005s.ctab <subjid> ?h |
stats/?h.aparc.a2005s.stats stats/aparc.annot.a2005s.ctab |
|
-aparc2aseg |
aseg.mgz |
["mri_aparc2aseg"] --s <subjid> --ribbon |
aparc+aseg.mgz |
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?h.ribbon.mgz |
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label/?h.aparc.annot |
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aseg.mgz |
["mri_aparc2aseg"] --s <subjid> --ribbon --a2005s |
aparc.a2005s+aseg.mgz |
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?h.ribbon.mgz |
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label/?h.aparc.a2005s.annot |
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-wmparc |
aparc+aseg.mgz |
["mri_aparc2aseg"] --s <subjid> --labelwm --hypo-as-wm --rip-unknown --ribbon --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz |
wmparc.mgz |
|
wmparc.mgz |
["mri_segstats"] --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject <subjid> --surf-wm-vol --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt |
wmparc.stats |
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.