| Deletions are marked like this. | Additions are marked like this. |
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| 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]. | Click [[ReconAllBlockDiagram|here]] to see this information presented in a block diagram format and [[ReconAllFilesVsSteps|here for a process v. files table]]. |
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||<|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|| |
||<|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|| |
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||<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'>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|| |
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| ||<rowbgcolor='#E0E0FF'>transforms/talairach.xfm||<bgcolor='#E0E0FF'>["talairach_afd"] -T 0.005 -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|| |
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||<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|| |
||<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|| |
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||<|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|| |
||<|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|| |
| Line 31: | Line 31: |
| ||<|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|| | ||<|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|| |
| Line 34: | Line 34: |
| ||<|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|| | ||<|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|| |
| Line 37: | Line 37: |
| ||<|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|| | ||<|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|| |
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| ||<|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|| | ||<|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|| |
| Line 42: | Line 42: |
| ||<|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|| | ||<|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|| |
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| ||<|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|| | ||<|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|| |
| Line 47: | Line 47: |
| ||<|2(bgcolor='#FFFFE0'>-ccseg||<bgcolor='#E0E0FF'>aseg.mgz||<|1(bgcolor='#E0E0FF'>["mri_cc"] -aseg aseg.auto.mgz -o aseg.auto_CCseg.mgz <subjid>||<bgcolor='#E0E0FF'>aseg.auto_CCseg.mgz|| | ||<|2(bgcolor='#FFFFE0'>-ccseg||<bgcolor='#E0E0FF'>aseg.mgz||<|1(bgcolor='#E0E0FF'>[[mri_cc]] -aseg aseg.auto.mgz -o aseg.auto_CCseg.mgz <subjid>||<bgcolor='#E0E0FF'>aseg.auto_CCseg.mgz|| |
| Line 49: | Line 49: |
| ||<|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|| | ||<|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|| |
| Line 52: | Line 52: |
| ||<|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|| | ||<|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|| |
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||<|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|| |
||<|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|| |
| Line 58: | Line 58: |
| ||<bgcolor='#E0E0FF'>wm.asegedit.mgz||<|2(bgcolor='#E0E0FF'>["mri_pretess"] wm.asegedit.mgz wm norm.mgz wm.mgz||<|2(bgcolor='#E0E0FF'>wm.mgz|| | ||<bgcolor='#E0E0FF'>wm.asegedit.mgz||<|2(bgcolor='#E0E0FF'>[[mri_pretess]] wm.asegedit.mgz wm norm.mgz wm.mgz||<|2(bgcolor='#E0E0FF'>wm.mgz|| |
| Line 60: | Line 60: |
| ||<|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|| | ||<|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|| |
| Line 63: | Line 63: |
| ||<|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|| | ||<|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|| |
| Line 65: | Line 65: |
|
||<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'>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|| |
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||<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'>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|| |
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||<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|| |
||<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|| |
| Line 76: | Line 76: |
|
||<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'>?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|| |
| Line 80: | Line 80: |
| ||<|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|| | ||<|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|| |
| Line 87: | Line 87: |
| ||<|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|| | ||<|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|| |
| Line 89: | Line 89: |
|
||<|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|| |
||<|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|| |
| Line 92: | Line 92: |
|
||<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|| |
||<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|| |
| Line 95: | Line 95: |
| ||<|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|| | ||<|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|| |
| Line 97: | Line 97: |
|
||<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|| |
||<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|| |
| Line 102: | Line 102: |
|
||<|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|| |
||<|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|| |
| Line 107: | Line 107: |
|
||<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|| |
||<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|| |
| Line 110: | Line 110: |
|
||<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|| |
||<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|| |
| Line 113: | Line 113: |
|
||<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|| |
||<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|| |
| Line 117: | Line 117: |
| ||<bgcolor='#E0E0FF'> aseg.mgz ||<|3(bgcolor='#E0E0FF'>["mri_aparc2aseg"] --s <subjid> --ribbon --a2005s||<|3(bgcolor='#E0E0FF'> aparc.a2005s+aseg.mgz|| | ||<bgcolor='#E0E0FF'> aseg.mgz ||<|3(bgcolor='#E0E0FF'>[[mri_aparc2aseg]] --s <subjid> --ribbon --a2005s||<|3(bgcolor='#E0E0FF'> aparc.a2005s+aseg.mgz|| |
| Line 120: | Line 120: |
|
||<|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|| |
||<|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|| |
FreeSurfer Tutorial: Process Flow
This table shows the recon-all steps for the latest stable version of FreeSurfer, v4.0.2. See ReconAllDevTable for the dev 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 |
||
-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.auto.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 |
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?h.white |
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?h.pial |
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recon-all -autorecon3 -subjid <subjid> |
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-sphere |
?h.inflated |
mris_sphere ?h.inflated ?h.sphere |
?h.sphere |
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-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 |
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-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 |
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-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 |
|
?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 |
|
?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 |