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| ||<|14(bgcolor='#FFFFE0'>'''["recon-all"] -autorecon1 -subjid subj'''|| | ||<|17(bgcolor='#FFFFE0'>'''["recon-all"] -autorecon1 -subjid subj'''|| |
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| ||<rowbgcolor='#E0E0FF'>||awk -f $FREESURFER_HOME/bin/extract_talairach_avi_QA.awk <transforms/talairach_avi.log||<bgcolor='#E0E0FF'>transforms/talairach_avi.log|| | ||<rowbgcolor='#E0E0FF'>||awk -f $FREESURFER_HOME/bin/extract_talairach_avi_QA.awk transforms/talairach_avi.log||<bgcolor='#E0E0FF'>transforms/talairach_avi.log|| |
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| ||<|2(bgcolor='#FFFFE0'>-skullstrip||<bgcolor='#E0E0FF'>T1.mgz||<bgcolor='#E0E0FF'>["mri_watershed"] -keep brainmask.auto.mgz brainmask.mgz brainmask.mgz -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|| | ||<|4(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"] -brain_atlas $FREESURFER_HOME/average/RB_all_withskull_2007-08-08.gca transforms/talairach_with_skull.lta -h 5 orig.mgz brainmask.auto.mgz||<bgcolor='#E0E0FF'>brainmask.auto.mgz|| ||<rowbgcolor='#E0E0FF'>T1.mgz||bgcolor='#E0E0FF'>["mri_mask"] T1.mgz brainmask.auto.mgz brainmask.auto.mgz ||<bgcolor='#E0E0FF'>brainmask.mgz|| |
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FreeSurfer Tutorial: Process Flow
Click [wiki:ReconAllBlockDiagram here] to see this information presented in a block diagram format and [wiki:ReconAllFilesVsSteps here for a process v. files table].
See also the OtherUsefulFlags for other recon-all options.
recon-all step |
Individual Flag |
Input |
Command Line |
Output |
["recon-all"] -autorecon1 -subjid subj |
||||
-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 |
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-motioncor |
orig/001.mgz |
["mri_motion_correct.fsl"] -o rawavg.mgz -wild orig/001.mgz orig/002.mgz |
rawavg.mgz |
|
orig/002.mgz |
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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 |
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-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 |
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transforms/talairach.xfm |
["talairach_afd"] -T 0.005 -xfm transforms/talairach.xfm |
transforms/talairach.xfm |
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awk -f $FREESURFER_HOME/bin/extract_talairach_avi_QA.awk transforms/talairach_avi.log |
transforms/talairach_avi.log |
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-normalization |
nu.mgz |
["mri_normalize"] -g 1 nu.mgz T1.mgz |
T1.mgz |
||<|4(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
T1.mgz |
["mri_watershed"] -brain_atlas $FREESURFER_HOME/average/RB_all_withskull_2007-08-08.gca transforms/talairach_with_skull.lta -h 5 orig.mgz brainmask.auto.mgz |
brainmask.auto.mgz |
T1.mgz |
bgcolor='#E0E0FF'>["mri_mask"] T1.mgz brainmask.auto.mgz brainmask.auto.mgz |
brainmask.mgz |
brainmask.auto.mgz |
cp brainmask.auto.mgz brainmask.mgz |
brainmask.mgz |
["recon-all"] -autorecon2 -subjid subj |
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-gcareg |
brainmask.mgz |
["mri_em_register"] -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB_all_2006-02-15.gca transforms/talairach.lta |
transforms/talairach.lta |
|
nu.mgz |
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-canorm |
brainmask.mgz |
["mri_ca_normalize"] -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB_all_2006-02-15.gca transforms/talairach.lta norm.mgz |
norm.mgz |
|
nu.mgz |
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transforms/talairach.lta |
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-careg |
brainmask.mgz |
["mri_ca_register"] -align -mask brainmask.mgz -T transforms/talairach.lta norm.mgz $FREESURFER_HOME/average/RB_all_2006-02-15.gca transforms/talairach.m3z |
transforms/talairach.m3z |
|
transforms/talairach.lta |
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norm.mgz |
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-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 |
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transforms/talairach.m3z.inv.z.mgz |
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-rmneck |
nu.mgz |
["mri_remove_neck"] -radius 25 nu.mgz transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2006-02-15.gca nu_noneck.mgz |
nu_noneck.mgz |
|
transforms/talairach.m3z |
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-skull-lta |
transforms/talairach.lta |
["mri_em_register"] -skull -t transforms/talairach.lta nu_noneck.mgz $FREESURFER_HOME/average/RB_all_withskull_2006-02-15.gca transforms/talairach_with_skull.lta |
transforms/talairach_with_skull.lta |
|
nu_noneck.mgz |
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-calabel |
norm.mgz |
["mri_ca_label"] -align norm.mgz transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2006-02-15.gca aseg.auto.mgz |
aseg.auto.mgz |
|
transforms/talairach.m3z |
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aseg.auto.mgz |
cp aseg.auto.mgz aseg.mgz |
aseg.mgz |
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-normalization2 |
brainmask.mgz |
["mri_normalize"] -mask brainmask.mgz -aseg aseg.mgz norm.mgz brain.mgz |
brain.mgz |
|
norm.mgz |
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brain.mgz |
["mri_mask"] brain.mgz brainmask.mgz brain.finalsurfs.mgz |
brain.finalsurfs.mgz |
||
brainmask.mgz |
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-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 |
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aseg.mgz |
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brain.mgz |
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wm.asegedit.mgz |
["mri_pretess"] wm.asegedit.mgz wm norm.mgz wm.mgz |
wm.mgz |
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norm.mgz |
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-fill |
wm.mgz |
["mri_fill"] -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.mgz wm.mgz filled.mgz |
filled.mgz |
|
aseg.mgz |
../scripts/ponscc.cut.log |
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transforms/talairach.lta |
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-tessellate |
filled.mgz |
["mri_tessellate"] filled.mgz 255 ../surf/lh.orig.nofix |
lh.orig.nofix |
|
["mri_tessellate"] filled.mgz 127 ../surf/rh.orig.nofix |
rh.orig.nofix |
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-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 -0 ?h.inflated.nofix ?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 |
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?h.qsphere.nofix |
["mris_fix_topology"] -errors -mgz -sphere qsphere.nofix -ga <subjid> ?h |
?h.orig |
||
-finalsurfs |
brain.finalsurfs.mgz |
["mris_make_surfaces"] -mgz -w 0 -T1 brain.finalsurfs.mgz subj ?h |
?h.white |
|
?h.pial |
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?h.thickness |
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?h.orig |
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?h.curv |
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?h.area, ?h.cortex.label |
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-smooth2 |
?h.white |
["mris_smooth"] ?h.white ?h.smoothwm |
?h.smoothwm |
|
-inflate2 |
?h.white |
["mris_inflate"] ?h.white ?h.inflated |
?h.inflated |
|
?h.sulc |
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-segstats |
aseg.mgz |
["mri_segstats"] --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --ctab $FREESURFER_HOME/ASegStatsLUT.txt --subject <subjid> |
stats/aseg.stats |
|
-cortribbon |
orig.mgz |
["mris_volmask"] --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance <subjid> |
?h.ribbon.mgz |
|
?h.white |
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?h.pial |
||||
["recon-all"] -autorecon3 -subjid subj |
||||
-sphere |
?h.inflated |
["mris_sphere"] ?h.inflated ?h.sphere |
?h.sphere |
|
-surfreg |
?h.sphere |
["mris_register"] -curv ?h.sphere $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif ?h.sphere.reg |
?h.sphere.reg |
|
-jacobian_white |
?h.white, ?h.sphere.reg |
["mris_jacobian"] ../surf/?h.white ../surf/?h.sphere.reg ../surf/?h.jacobian_white |
?h.jacobian_white |
|
-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, ?h.sphere.reg |
["mris_ca_label"] -aseg ../mri/aseg.mgz <subjid> ?h ../surf/?h.sphere.reg $FREESURFER_HOME/average/?h.curvature.buckner40.filled.desikan_killiany.gcs ../label/?h.aparc.annot |
label/?h.aparc.annot |
|
-parcstats |
label/?h.aparc.annot |
["mris_anatomical_stats"] -mgz -f stats/?h.aparc.stats -b -a label/?h.aparc.annot -c stats/aparc.annot.ctab subj ?h |
stats/?h.aparc.stats label/aparc.annot.ctab |
|
-cortparc2 |
aseg.mgz, ?h.sphere.reg |
["mris_ca_label"] -aseg ../mri/aseg.mgz <subjid> ?h ../surf/?h.sphere.reg $FREESURFER_HOME/average/?h.atlas2005_simple.gcs ../label/?h.aparc.a2005s.annot |
label/?h.aparc.a2005s.annot |
|
-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 subj ?h |
stats/?h.aparc.a2005s.stats stats/aparc.annot.a2005s.ctab |
|
-aparc2aseg |
aseg.mgz |
["mri_aparc2aseg"] --s subj --ribbon |
aparc+aseg.mgz |
|
?h.ribbon.mgz |
||||
label/?h.aparc.annot |
||||
-wmparc |
aparc+aseg.mgz |
["mri_aparc2aseg"] --s subj --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 |