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Size: 16021
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| Deletions are marked like this. | Additions are marked like this. |
| Line 29: | Line 29: |
| ||<|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|| | ||<|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|| |
| Line 40: | Line 40: |
| ||<|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|| |
| Line 44: | Line 44: |
| ||<|4(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_noCCseg.mgz||<|2(bgcolor='#E0E0FF'>aseg.auto_noCCseg.mgz|| | ||<|4(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_noCCseg.mgz||<|2(bgcolor='#E0E0FF'>aseg.auto_noCCseg.mgz|| |
| Line 48: | Line 48: |
| ||<|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 51: | Line 51: |
| ||<|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|| |
| Line 53: | Line 53: |
| ||<|6(bgcolor='#FFFFE0'>-segmentation||<bgcolor='#E0E0FF'>brain.mgz||<bgcolor='#E0E0FF'>[[mri_segment]] brain.mgz wm.seg.mgz||<bgcolor='#E0E0FF'>wm.seg.mgz|| | ||<|6(bgcolor='#FFFFE0'>-[[segmentation]]||<bgcolor='#E0E0FF'>brain.mgz||<bgcolor='#E0E0FF'>[[mri_segment]] brain.mgz wm.seg.mgz||<bgcolor='#E0E0FF'>wm.seg.mgz|| |
| Line 59: | Line 59: |
| ||<|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_noCCseg.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_noCCseg.mgz wm.mgz filled.mgz||<bgcolor='#E0E0FF'>filled.mgz|| |
| Line 62: | Line 62: |
| ||<|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 70: | Line 70: |
| ||<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='#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|| |
| Line 79: | Line 79: |
| ||<|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 86: | Line 86: |
| ||<|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 91: | Line 91: |
| ||<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 96: | Line 96: |
| ||<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: |
| ||<bgcolor='#FFFFE0'>-sphere||<bgcolor='#E0E0FF'>?h.inflated,?h.smoothwm||<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|| |
||<bgcolor='#FFFFE0'>-[[sphere]]||<bgcolor='#E0E0FF'>?h.inflated,?h.smoothwm||<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 106: | Line 106: |
| ||<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 109: | Line 109: |
| ||<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 112: | Line 112: |
| ||<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 119: | Line 119: |
| ||<|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|| | ||<|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|| |
FreeSurfer Tutorial: Process Flow
This table shows the recon-all steps for the current dev version of FreeSurfer. See ReconAllStableTablev4 to see a process flow for the latest stable version of FreeSurfer.
Click here to see this information presented in a block diagram format and here for a process v. files table.
See also the OtherUsefulFlags for other recon-all options.
recon-all step |
Individual Flag |
Input |
Command Line |
Output |
recon-all -autorecon1 -subjid <subjid> |
||||
-i <invol1> -i <invol2> |
invol1.dcm |
mri_convert invol1.dcm orig/001.mgz |
orig/001.mgz |
|
invol2.dcm |
mri_convert invol2.dcm orig/002.mgz |
orig/002.mgz |
||
orig/001.mgz |
mri_motion_correct.fsl -o rawavg.mgz -wild orig/001.mgz orig/002.mgz |
rawavg.mgz |
||
orig/002.mgz |
||||
rawavg.mgz |
mri_convert rawavg.mgz orig.mgz --conform |
orig.mgz |
||
orig.mgz |
mri_add_xform_to_header -c transforms/talairach.xfm orig.mgz orig.mgz |
orig.mgz |
||
orig.mgz |
mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 |
nu.mgz |
||
nu.mgz |
talairach_avi --i nu.mgz --xfm transforms/talairach.auto.xfm |
transforms/talairach.auto.xfm |
||
transforms/talairach.auto.xfm |
cp transforms/talairach.auto.xfm transforms/talairach.xfm |
transforms/talairach.xfm |
||
transforms/talairach.xfm |
talairach_afd -T 0.005 -xfm transforms/talairach.xfm |
transforms/talairach.xfm |
||
awk -f $FREESURFER_HOME/bin/extract_talairach_avi_QA.awk transforms/talairach_avi.log |
transforms/talairach_avi.log |
|||
nu.mgz |
mri_normalize -g 1 nu.mgz T1.mgz |
T1.mgz |
||
nu.mgz |
mri_em_register -skull nu.mgz $FREESURFER_HOME/average/RB_all_withskull_2007-08-08.gca transforms/talairach_with_skull.lta |
transforms/talairach_with_skull.lta |
||
T1.mgz |
mri_watershed -T1 -brain_atlas $FREESURFER_HOME/average/RB_all_withskull_2007-08-08.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz |
brainmask.auto.mgz |
||
brainmask.auto.mgz |
cp brainmask.auto.mgz brainmask.mgz |
brainmask.mgz |
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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 |
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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 |
||||
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 |
||
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> |
||||
?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.atlas2005_simple.gcs label/?h.aparc.a2005s.annot |
label/?h.aparc.a2005s.annot |
||
?h.sphere.reg |
||||
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 |
||
aseg.mgz |
mri_aparc2aseg --s <subjid> --ribbon |
aparc+aseg.mgz |
||
?h.ribbon.mgz |
||||
label/?h.aparc.annot |
||||
aseg.mgz |
mri_aparc2aseg --s <subjid> --ribbon --a2005s |
aparc.a2005s+aseg.mgz |
||
?h.ribbon.mgz |
||||
label/?h.aparc.a2005s.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.