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Size: 14825
Comment: removed colors
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Size: 13608
Comment: update mri_segstats command line
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| ||<style="text-align: left;" |16>'''[[recon-all]] -autorecon1 -subjid <subjid>''' || ||<style="text-align: left;" |2>-i <invol1> -i <invol2> ||<#000eff>invol1.dcm ||<#000eff>[[mri_convert]] invol1.dcm orig/001.mgz ||<#000eff>orig/001.mgz || ||invol2.dcm ||<#000eff>[[mri_convert]] invol2.dcm orig/002.mgz ||<#000eff>orig/002.mgz || ||<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 || |
||<style="text-align: left;" |18>'''[[recon-all]] -autorecon1 -subjid <subjid>''' || ||<style="text-align: left;" |2>-i <invol1> -i <invol2> ||invol1.dcm ||[[mri_convert]] invol1.dcm orig/001.mgz ||orig/001.mgz || ||invol2.dcm ||[[mri_convert]] invol2.dcm orig/002.mgz ||orig/002.mgz || ||<style="text-align: left;" |4>-[[motioncor]] ||orig/001.mgz ||<style="text-align: left;" |2>[[mri_motion_correct.fsl]] -o rawavg.mgz -wild orig/001.mgz orig/002.mgz ||<style="text-align: left;" |2>rawavg.mgz || |
| Line 16: | Line 16: |
| ||-[[nuintensitycor]] ||<#000eff>orig.mgz ||<#000eff>[[mri_nu_correct.mni]] --i orig.mgz --o nu.mgz --n 2 ||<#000eff>nu.mgz || ||<style="text-align: left;" |4>-[[talairach]] ||<#000eff>nu.mgz ||<#000eff>[[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 ||<#000eff>transforms/talairach.xfm || ||transforms/talairach.xfm ||<#000eff>[[talairach_afd]] -T 0.005 -xfm transforms/talairach.xfm ||<#000eff>transforms/talairach.xfm || ||||awk -f $FREESURFER_HOME/bin/extract_talairach_avi_QA.awk transforms/talairach_avi.log ||<#000eff>transforms/talairach_avi.log || ||-[[normalization]] ||<#000eff>nu.mgz ||<#000eff>[[mri_normalize]] -g 1 nu.mgz T1.mgz ||<#000eff>T1.mgz || ||<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 || ||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 || ||brainmask.auto.mgz ||cp brainmask.auto.mgz brainmask.mgz ||<#000eff>brainmask.mgz || || ||<#000eff> ||<#000eff> ||<#000eff> ||<#000eff> || |
||-[[nuintensitycor]] ||orig.mgz ||[[mri_nu_correct.mni]] --i orig.mgz --o nu.mgz --n 2 ||nu.mgz || ||<style="text-align: left;" |4>-[[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 || ||<style="text-align: left;" |5>-[[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 || ||T1.mgz||<style="text-align: left;"|2>mri_gcut -110 -mult brainmask.auto.mgz T1.mgz brainmask.auto.mgz ||<style="text-align: left;"|2>brainmask.auto.mgz|| ||brainmask.auto.mgz|| ||brainmask.auto.mgz ||cp brainmask.auto.mgz brainmask.mgz ||brainmask.mgz || || || || || || || |
| Line 27: | Line 29: |
| ||<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 || | ||<style="text-align: left;" |2>-[[gcareg]] ||brainmask.mgz ||<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 ||<style="text-align: left;" |2>transforms/talairach.lta || |
| Line 29: | Line 31: |
| ||<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 || | ||<style="text-align: left;" |3>-[[canorm]] ||brainmask.mgz ||<style="text-align: left;" |3>[[mri_ca_normalize]] -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB_all_2007-08-08.gca transforms/talairach.lta norm.mgz ||<style="text-align: left;" |3>norm.mgz || |
| Line 32: | Line 34: |
| ||<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 || | ||<style="text-align: left;" |3>-[[careg]] ||brainmask.mgz ||<style="text-align: left;" |3>[[mri_ca_register]] -align-after -nobigventricles -mask brainmask.mgz -T transforms/talairach.lta norm.mgz $FREESURFER_HOME/average/RB_all_2007-08-08.gca transforms/talairach.m3z ||<style="text-align: left;" |3>transforms/talairach.m3z || |
| Line 35: | Line 37: |
| ||<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 || | ||<style="text-align: left;" |3>-[[careginv]] ||<style="text-align: left;" |3>transforms/talairach.m3z ||<style="text-align: left;" |3>[[mri_ca_register]] -invert-and-save transforms/talairach.m3z ||transforms/talairach.m3z.inv.x.mgz || |
| Line 38: | Line 40: |
| ||<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 || | ||<style="text-align: left;" |2>-[[rmneck]] ||nu.mgz ||<style="text-align: left;" |2>[[mri_remove_neck]] -radius 25 nu.mgz transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2007-08-08.gca nu_noneck.mgz ||<style="text-align: left;" |2>nu_noneck.mgz || |
| Line 40: | Line 42: |
| ||<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 || | ||<style="text-align: left;" |2>-[[skull-lta]] ||transforms/talairach.lta ||<style="text-align: left;" |2>[[mri_em_register]] -skull -t transforms/talairach.lta nu_noneck.mgz $FREESURFER_HOME/average/RB_all_withskull_2007-08-08.gca transforms/talairach_with_skull.lta ||<style="text-align: left;" |2>transforms/talairach_with_skull.lta || |
| Line 42: | Line 44: |
| ||<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 || | ||<style="text-align: left;" |4>-[[calabel]] ||norm.mgz ||<style="text-align: left;" |2>[[mri_ca_label]] -align -nobigventricles norm.mgz transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2007-08-08.gca aseg.auto_noCCseg.mgz ||<style="text-align: left;" |2>aseg.auto_noCCseg.mgz || |
| Line 44: | Line 46: |
| ||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 || ||aseg.auto.mgz ||<#000eff>cp aseg.auto.mgz aseg.mgz ||<#000eff>aseg.mgz || ||<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 || |
||aseg.auto_noCCseg.mgz ||<style="text-align: left;" |1>[[mri_cc]] -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz <subjid> ||aseg.auto.mgz || ||aseg.auto.mgz ||cp aseg.auto.mgz aseg.mgz ||aseg.mgz || ||<style="text-align: left;" |3>-[[normalization2]] ||brainmask.mgz ||<style="text-align: left;" |3>[[mri_normalize]] -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz ||<style="text-align: left;" |3>brain.mgz || |
| Line 49: | Line 51: |
| ||<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 || | ||<style="text-align: left;" |2>-[[maskbfs]] ||brain.mgz ||<style="text-align: left;" |2>[[mri_mask]] -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz ||<style="text-align: left;" |2>brain.finalsurfs.mgz || |
| Line 51: | Line 53: |
| ||<style="text-align: left;" |6>-[[segmentation]] ||<#000eff>brain.mgz ||<#000eff>[[mri_segment]] brain.mgz wm.seg.mgz ||<#000eff>wm.seg.mgz || ||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 || |
||<style="text-align: left;" |6>-[[segmentation]] ||brain.mgz ||[[mri_segment]] brain.mgz wm.seg.mgz ||wm.seg.mgz || ||wm.seg.mgz ||<style="text-align: left;" |3>[[mri_edit_wm_with_aseg]] wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz ||<style="text-align: left;" |3>wm.asegedit.mgz || |
| Line 55: | Line 57: |
| ||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 || | ||wm.asegedit.mgz ||<style="text-align: left;" |2>[[mri_pretess]] wm.asegedit.mgz wm norm.mgz wm.mgz ||<style="text-align: left;" |2>wm.mgz || |
| Line 57: | Line 59: |
| ||<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 || ||aseg.auto_noCCseg.mgz ||<#000eff style="text-align: left;" |2>../scripts/ponscc.cut.log || |
||<style="text-align: left;" |3>-[[fill]] ||wm.mgz ||<style="text-align: left;" |3>[[mri_fill]] -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz ||filled.mgz || ||aseg.auto_noCCseg.mgz ||<style="text-align: left;" |2>../scripts/ponscc.cut.log || |
| Line 60: | Line 62: |
| ||<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 || | ||<style="text-align: left;" |8>-[[tessellate]] ||filled.mgz ||<style="text-align: left;" |2>[[mri_pretess]] filled.mgz 255 norm.mgz filled-pretess255.mgz ||<style="text-align: left;" |2>filled-pretess255.mgz || |
| Line 62: | Line 64: |
| ||filled-pretess255.mgz ||<#000eff>[[mri_tessellate]] filled-pretess255.mgz 255 lh.orig.nofix ||<#000eff>lh.orig.nofix || ||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 || |
||filled-pretess255.mgz ||[[mri_tessellate]] filled-pretess255.mgz 255 lh.orig.nofix ||lh.orig.nofix || ||filled.mgz ||<style="text-align: left;" |2>[[mri_pretess]] filled.mgz 127 norm.mgz filled-pretess127.mgz ||<style="text-align: left;" |2>filled-pretess127.mgz || |
| Line 65: | Line 67: |
| ||filled-pretess127.mgz ||<#000eff>[[mri_tessellate]] filled-pretess127.mgz 127 rh.orig.nofix ||<#000eff>rh.orig.nofix || ||?h.orig.nofix ||<#000eff>[[mris_extract_main_component]] ?h.orig.nofix ?h.orig.nofix ||<#000eff>?h.orig.nofix || ||||<#000eff>rm -f filled-pretess255.mgz filled-pretess127.mgz ||<#000eff> || ||-[[smooth|smooth1]] ||<#000eff>?h.orig.nofix ||<#000eff>[[mris_smooth]] -nw ?h.orig.nofix ?h.smoothwm.nofix ||<#000eff>?h.smoothwm.nofix || ||-[[inflate|inflate1]] ||<#000eff>?h.smoothwm.nofix ||<#000eff>[[mris_inflate]] -no-save-sulc ?h.smoothwm.nofix ?h.inflated.nofix ||<#000eff>?h.inflated.nofix || ||-[[qsphere]] ||<#000eff>?h.inflated.nofix ||<#000eff>[[mris_sphere]] -q ?h.inflated.nofix ?h.qsphere.nofix ||<#000eff>?h.qsphere.nofix || ||<style="text-align: left;" |6>-[[fix]] ||<#000eff>?h.orig.nofix ||<#000eff>cp ?h.orig.nofix ?h.orig ||<#000eff>?h.orig || ||?h.inflated.nofix ||<#000eff>cp ?h.inflated.nofix ?h.inflated ||<#000eff>?h.inflated || ||?h.qsphere.nofix ||<#000eff>[[mris_fix_topology]] -mgz -sphere qsphere.nofix -ga <subjid> ?h ||<#000eff>?h.orig || ||?h.orig ||<#000eff>[[mris_euler_number]] ?h.orig ||<#000eff>?h.orig || ||?h.orig ||<#000eff>[[mris_remove_intersection]] ?h.orig ?h.orig ||<#000eff>?h.orig || || ||<#000eff>rm ?h.inflated ||<#000eff> || ||<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 || |
||filled-pretess127.mgz ||[[mri_tessellate]] filled-pretess127.mgz 127 rh.orig.nofix ||rh.orig.nofix || ||?h.orig.nofix ||[[mris_extract_main_component]] ?h.orig.nofix ?h.orig.nofix ||?h.orig.nofix || || ||rm -f filled-pretess255.mgz filled-pretess127.mgz || || ||-[[smooth|smooth1]] ||?h.orig.nofix ||[[mris_smooth]] -nw ?h.orig.nofix ?h.smoothwm.nofix ||?h.smoothwm.nofix || ||-[[inflate|inflate1]] ||?h.smoothwm.nofix ||[[mris_inflate]] -no-save-sulc ?h.smoothwm.nofix ?h.inflated.nofix ||?h.inflated.nofix || ||-[[qsphere]] ||?h.inflated.nofix ||[[mris_sphere]] -q ?h.inflated.nofix ?h.qsphere.nofix ||?h.qsphere.nofix || ||<style="text-align: left;" |6>-[[fix]] ||?h.orig.nofix ||cp ?h.orig.nofix ?h.orig ||?h.orig || ||?h.inflated.nofix ||cp ?h.inflated.nofix ?h.inflated ||?h.inflated || ||?h.qsphere.nofix ||[[mris_fix_topology]] -mgz -sphere qsphere.nofix -ga <subjid> ?h ||?h.orig || ||?h.orig ||[[mris_euler_number]] ?h.orig ||?h.orig || ||?h.orig ||[[mris_remove_intersection]] ?h.orig ?h.orig ||?h.orig || || ||rm ?h.inflated || || ||<style="text-align: left;" |7>-[[finalsurfs]] ||<style="text-align: left;" |3>brain.finalsurfs.mgz ||<style="text-align: left;" |7>[[mris_make_surfaces]] -noaparc -mgz -T1 brain.finalsurfs <subjid> ?h ||?h.white || |
| Line 84: | Line 86: |
| ||<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 || | ||<style="text-align: left;" |5>-[[surfvolume]] ||<style="text-align: left;" |1>?h.area ||<style="text-align: left;" |2>[[mris_calc]] -o ?h.area.mid ?h.area add ?h.area.pial ||<style="text-align: left;" |2>?h.area.mid || |
| Line 86: | Line 88: |
| ||<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 || ||<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 || |
||<style="text-align: left;" |1>?h.area.mid ||<style="text-align: left;" |1>[[mris_calc]] -o ?h.area.mid ?h.area.mid div 2 ||?h.area.mid || ||<style="text-align: left;" |1>?h.area.mid ||<style="text-align: left;" |2>[[mris_calc]] -o ?h.volume ?h.area.mid mul ?h.thickness ||<style="text-align: left;" |2>?h.volume || |
| Line 89: | Line 91: |
| ||-[[smooth|smooth2]] ||<#000eff>?h.white ||<#000eff>[[mris_smooth]] -n 3 -nw ?h.white ?h.smoothwm ||<#000eff>?h.smoothwm || ||<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 || |
||-[[smooth|smooth2]] ||?h.white ||[[mris_smooth]] -n 3 -nw ?h.white ?h.smoothwm ||?h.smoothwm || ||<style="text-align: left;" |4>-[[inflate|inflate2]] ||<style="text-align: left;" |2>?h.smoothwm ||<style="text-align: left;" |2>[[mris_inflate]] ?h.smoothwm ?h.inflated ||?h.inflated || |
| Line 92: | Line 94: |
| ||<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 ||?h.inflated.H || | ||<style="text-align: left;" |2>?h.inflated ||<style="text-align: left;" |2>[[mris_curvature]] -thresh .999 -n -a 5 -w -distances 10 10 ?h.inflated ||?h.inflated.H || |
| Line 94: | Line 96: |
| || ||<#000eff> ||<#000eff> ||<#000eff> ||<#000eff> || | || || || || || || |
| Line 96: | Line 98: |
| ||-[[sphere]] ||<#000eff>?h.inflated,?h.smoothwm ||<#000eff>[[mris_sphere]] ?h.inflated ?h.sphere ||<#000eff>?h.sphere || ||-[[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 || ||<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 || |
||-[[sphere]] ||?h.inflated,?h.smoothwm ||[[mris_sphere]] ?h.inflated ?h.sphere ||?h.sphere || ||-[[surfreg]] ||?h.sphere ||[[mris_register]] -curv ?h.sphere $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif ?h.sphere.reg ||?h.sphere.reg || ||<style="text-align: left;" |2>-[[jacobian_white]] ||?h.white ||<style="text-align: left;" |2>[[mris_jacobian]] ?h.white ?h.sphere.reg ?h.jacobian_white ||<style="text-align: left;" |2>?h.jacobian_white || |
| Line 100: | Line 102: |
| ||-[[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 || ||<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 || |
||-[[avgcurv]] ||?h.sphere.reg ||[[mrisp_paint]] -a 5 $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif#6 ?h.sphere.reg ?h.avg_curv ||?h.avg_curv || ||<style="text-align: left;" |2>-[[cortparc]] ||aseg.mgz ||<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 ||<style="text-align: left;" |2>label/?h.aparc.annot || |
| Line 103: | Line 105: |
| ||-[[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 || ||<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 || |
||-[[parcstats]] ||label/?h.aparc.annot ||[[mris_anatomical_stats]] -mgz -f stats/?h.aparc.stats -b -a label/?h.aparc.annot -c label/aparc.annot.ctab <subjid> ?h ||stats/?h.aparc.stats label/aparc.annot.ctab || ||<style="text-align: left;" |2>-[[cortparc|cortparc2]] ||aseg.mgz ||<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 ||<style="text-align: left;" |2>label/?h.aparc.a2009s.annot || |
| Line 106: | Line 108: |
| ||-[[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 || ||-[[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 || ||<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 || |
||-[[parcstats|parcstats2]] ||label/?h.aparc.a2009s.annot ||[[mris_anatomical_stats]] -mgz -f stats/?h.aparc.a2009s.stats -b -a label/?h.aparc.a2009s.annot -c label/aparc.annot.a2009s.ctab <subjid> ?h ||stats/?h.aparc.a2009s.stats stats/aparc.annot.a2009s.ctab || ||<style="text-align: left;" |3>-[[cortribbon]] ||aseg.mgz ||<style="text-align: left;" |3>[[mris_volmask]] --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance <subjid> ||<style="text-align: left;" |3>?h.ribbon.mgz || |
| Line 111: | Line 112: |
| ||<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 || | ||-[[segstats]] ||aseg.mgz ||[[mri_segstats]] --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supertent --subcortgray --totalgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --ctab $FREESURFER_HOME/ASegStatsLUT.txt --subject <subjid>||stats/aseg.stats || ||<style="text-align: left;" |6>-[[aparc2aseg]] ||aseg.mgz ||<style="text-align: left;" |3>[[mri_aparc2aseg]] --s <subjid> --ribbon ||<style="text-align: left;" |3>aparc+aseg.mgz || |
| Line 114: | Line 116: |
| ||aseg.mgz ||<#000eff style="text-align: left;" |3>[[mri_aparc2aseg]] --s <subjid> --ribbon --a2009s ||<#000eff style="text-align: left;" |3>aparc.a2009s+aseg.mgz || | ||aseg.mgz ||<style="text-align: left;" |3>[[mri_aparc2aseg]] --s <subjid> --ribbon --a2009s ||<style="text-align: left;" |3>aparc.a2009s+aseg.mgz || |
| Line 117: | Line 119: |
| ||<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 || ||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 || |||||||||||| |
||<style="text-align: left;" |2>-[[wmparc]] ||aparc+aseg.mgz ||<style="text-align: left;" |1>[[mri_aparc2aseg]] --s <subjid> --labelwm --hypo-as-wm --rip-unknown --ribbon --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz ||<style="text-align: left;" |1>wmparc.mgz || ||wmparc.mgz ||<style="text-align: left;" |1>[[mri_segstats]] --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject <subjid> --surf-wm-vol --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt ||<style="text-align: left;" |1>stats/wmparc.stats || ||||||||||<style="text-align: center;"> || |
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 |
||
T1.mgz |
mri_gcut -110 -mult brainmask.auto.mgz T1.mgz brainmask.auto.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 |
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_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supertent --subcortgray --totalgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --ctab $FREESURFER_HOME/ASegStatsLUT.txt --subject <subjid> |
stats/aseg.stats |
||
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 |
||||
label/?h.aparc.a2009s.annot |
||||
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 |
stats/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.