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| ||<bgcolor='#E0E0FF'>?h.qsphere.nofix||<bgcolor='#E0E0FF'>["mris_fix_topology"] -errors -mgz -sphere qsphere.nofix -ga <subjid> ?h||<bgcolor='#E0E0FF'>?h.orig|| | ||<bgcolor='#E0E0FF'>?h.qsphere.nofix||<bgcolor='#E0E0FF'>["mris_fix_topology"] -errors -mgz -sphere qsphere.nofix -ga <subjid> ?h||<bgcolor='#E0E0FF'>?h.orig ?h.qsphere|| |
FreeSurfer Tutorial: Process Flow
Click [wiki:ReconAllBlockDiagram here] to see this information presented in a block diagram format and [http://grahamwideman.com/gw/brain/fs/fsunderstanding2006/processvsdata2006.htm 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 |
||
-nuintensitycor |
orig.mgz |
["mri_nu_correct.mni"] --i orig.mgz --o nu.mgz --n 2 |
nu.mgz |
|
-talairach |
nu.mgz |
["talairach"] --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 |
||
-normalization |
nu.mgz |
["mri_normalize"] -g 1 nu.mgz T1.mgz |
T1.mgz |
|
-skullstrip |
T1.mgz |
["mri_watershed"] -atlas 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 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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-segstats |
aseg.mgz |
["mri_segstats"] --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --in mri/norm.mgz --ctab-default --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in-intensity-name orig --in-intensity-units MR --etiv --subject <subjid> |
stats/aseg.stats |
|
-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 |
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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 |
||
?h.qsphere.nofix |
["mris_fix_topology"] -errors -mgz -sphere qsphere.nofix -ga <subjid> ?h |
?h.orig ?h.qsphere |
||
-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 |
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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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-cortribbon |
orig.mgz |
["mri_surf2vol"] --mkmask --hemi ?h --fillribbon --template orig.mgz --volregidentity subj --outvol ?h.ribbon.mgz |
?h.ribbon.mgz |
|
?h.white |
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?h.pial |
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["recon-all"] -autorecon3 -subjid subj |
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-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 |
|
-contrasurfreg |
rh.sphere |
["mris_register"] -curv -reverse rh.sphere $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif rh.lh.sphere.reg |
rh.lh.sphere.reg |
|
lh.sphere |
["mris_register"] -w 0 -curv -reverse lh.sphere $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif lh.rh.sphere.reg |
lh.rh.sphere.reg |
||
-avgcurv |
?h.sphere.reg |
["mrisp_paint"] -a 5 $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif#6 ?h.sphere.reg ?h.avg_curv |
?h.avg_curv |
|
-cortparc |
?h.sphere.reg |
["mris_ca_label"] subj ?h ?h.sphere.reg $FREESURFER_HOME/average/?h.curvature.buckner40.filled.desikan_killiany.gcs ?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 |
|
-cortparc2 |
?h.sphere.reg |
["mris_ca_label"] subj ?h ?h.sphere.reg $FREESURFER_HOME/average/?h.atlas2005_simple.gcs ?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 stats/aparc.annot.a2005s.ctab subj ?h |
stats/?h.aparc.a2005s.stats |
|
-aparc2aseg |
aseg.mgz |
mri_aparc2aseg --s subj --ribbon |
aparc+aseg.mgz |
|
?h.ribbon.mgz |
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label/?h.aparc.annot |