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Describe ReconAllTable here. |
== FreeSurfer Tutorial: Process Flow == ||<rowbgcolor='#80FF80'>'''recon-all step'''||'''Input'''||'''Command Line'''||'''Output'''|| ||<bgcolor='#FFFFE0'>none||<bgcolor='#E0E0FF'>file.dcm||<bgcolor='#E0E0FF'>["mri_convert"] file.dcm orig/001.mgz||<bgcolor='#E0E0FF'>orig/001.mgz|| ||<|10(bgcolor='#FFFFE0'>["recon-all"] -autorecon1 -subjid subj|| ||<rowbgcolor='#E0E0FF'>orig/001.mgz||<|2(>["mri_motion_correct2"] -i orig/001.mgz -i orig/002.mgz -o rawavg.mgz||<|2(>rawavg.mgz|| ||<rowbgcolor='#E0E0FF'>orig/002.mgz|| ||<rowbgcolor='#E0E0FF'>rawavg.mgz||["mri_convert"] rawavg.mgz orig.mgz --conform||orig.mgz|| ||<rowbgcolor='#E0E0FF'>orig.mgz||["mri_convert"] orig.mgz orig.mnc||orig.mnc|| ||<rowbgcolor='#E0E0FF'>orig.mnc||(4 iterations of) ["nu_correct"] -clobber nu0.mnc nu1.mnc||nu4.mnc|| ||<rowbgcolor='#E0E0FF'>nu4.mnc||["mri_convert"] nu4.mnc nu.mgz||nu.mgz|| ||<rowbgcolor='#E0E0FF'>nu.mgz||["talairach2"] subjid -mgz||transforms/talairach.xfm|| ||<rowbgcolor='#E0E0FF'>nu.mgz||["mri_normalize"] nu.mgz T1.mgz||T1.mgz|| ||<rowbgcolor='#E0E0FF'>T1.mgz||["mri_watershed"] T1.mgz brain.mgz||brain.mgz|| ||<-4(rowbgcolor='#FF8080'>Check skullstrip (brain.mgz), talairach (transforms/talairach.xfm), and normalization (brain.mgz or T1.mgz - mean wm voxel value = 110)|| ||<|35(bgcolor='#FFFFE0'>["recon-all"] -autorecon2 -subjid subj|| ||<rowbgcolor='#E0E0FF'>brain.mgz||<|2(>["mri_em_register"] -mask brain.mgz -p .5 -fsamples fsamples.mgz nu.mgz $GCA transforms/talairach.lta||<|2(>transforms/talairach.lta|| ||<rowbgcolor='#E0E0FF'>nu.mgz|| ||<rowbgcolor='#E0E0FF'>brain.mgz||<|3(>["mri_ca_normalize"] -mask brain.mgz nu.mgz $GCA transforms/talairach.lta norm.mgz||<|3(>norm.mgz|| ||<rowbgcolor='#E0E0FF'>nu.mgz|| ||<rowbgcolor='#E0E0FF'>transforms/talairach.lta|| ||<rowbgcolor='#E0E0FF'>brain.mgz||<|3(>["mri_ca_register"] -cross-sequence -mask brain.mgz -T transforms/talairach.lta norm.mgz $GCA transforms/talairach.m3z||<|3(>transforms/talairach.m3z|| ||<rowbgcolor='#E0E0FF'>transforms/talairach.lta|| ||<rowbgcolor='#E0E0FF'>norm.mgz|| ||<rowbgcolor='#E0E0FF'>norm.mgz||<|2(>["mri_ca_label"] -cross-sequence norm.mgz transforms/talairach.m3z $GCA aseg.mgz||<|2(>aseg.mgz|| ||<rowbgcolor='#E0E0FF'>transforms/talairach.m3z|| ||<rowbgcolor='#E0E0FF'>brain.mgz||<|2(>["mri_normalize"] -mask brain.mgz nu.mgz T1.mgz||<|2(>T1.mgz|| ||<rowbgcolor='#E0E0FF'>nu.mgz|| ||<rowbgcolor='#E0E0FF'>T1.mgz||<|2(>["mri_mask"] T1.mgz brain.mgz brain.mgz||<|2(>brain.mgz|| ||<rowbgcolor='#E0E0FF'>brain.mgz|| ||<rowbgcolor='#E0E0FF'>brain.mgz||["mri_segment"] brain.mgz wm.mgz||wm.mgz|| ||<rowbgcolor='#E0E0FF'>wm.mgz||<|2(>["mri_edit_wm_with_aseg"] wm.mgz aseg.mgz wm.mgz||<|2(>wm.mgz|| ||<rowbgcolor='#E0E0FF'>aseg.mgz|| ||<rowbgcolor='#E0E0FF'>wm.mgz||<|2(>["mri_fill"] -a ../scripts/ponscc.cut.log -xform transforms/talairach.xfm -segmentation aseg.mgz wm.mgz filled.mgz||filled.mgz|| ||<rowbgcolor='#E0E0FF'>aseg.mgz||../scripts/ponscc.cut.log|| ||<|2(rowbgcolor='#E0E0FF'>filled.mgz||["mri_tessellate"] filled.mgz 255 ../surf/lh.orig||lh.orig|| ||<rowbgcolor='#E0E0FF'>["mri_tessellate"] filled.mgz 128 ../surf/rh.orig||rh.orig|| ||<rowbgcolor='#E0E0FF'>?h.orig||["mris_smooth"] ?h.orig ?h.smoothwm||?h.smoothwm|| ||<rowbgcolor='#E0E0FF'>?h.smoothwm||["mris_inflate"] ?h.smoothwm ?h.inflated||?h.inflated|| ||<rowbgcolor='#E0E0FF'>?h.inflated||["mris_sphere"] -w 0 -inflate -in 200 -q ?h.inflated ?h.qsphere||?h.qsphere|| ||<rowbgcolor='#E0E0FF'>?h.qsphere||["mris_fix_topology"] subj ?h||?h.orig|| ||<rowbgcolor='#E0E0FF'>?h.orig||["mris_euler_number"] ?h.orig||?h.orig.euler|| ||<rowbgcolor='#E0E0FF'>?h.orig||["mris_smooth"] ?h.orig ?h.smoothwm||?h.smoothwm|| ||<rowbgcolor='#E0E0FF'>?h.smoothwm||["mris_inflate"] ?h.smoothwm ?h.inflated||?h.inflated|| ||<rowbgcolor='#E0E0FF'>brain.mgz||<|3(>["mris_make_surfaces"] -w 0 subj ?h||?h.white|| ||<|2(rowbgcolor='#E0E0FF'>?h.orig||?h.pial|| ||<rowbgcolor='#E0E0FF'>?h.thickness|| ||<rowbgcolor='#E0E0FF'>orig.mgz||<rowspan=3>["mri_surf2vol"] --mkmask --hemi ?h --fillribbon --template orig.mgz --volregidentity subj --outvol ?h.ribbon.mgz||<rowspan=3>?h.ribbon.mgz|| ||<rowbgcolor='#E0E0FF'>?h.white|| ||<rowbgcolor='#E0E0FF'>?h.pial|| ||<-4(rowbgcolor='#FF8080'>Check final surfaces '''["tkmedit]" subj wm.mgz ?h.white brain.mgz'''|| ||<|8(bgcolor='#FFFFE0'>["recon-all"] -autorecon3 -subjid subj|| ||<rowbgcolor='#E0E0FF'>?h.inflated||["mris_sphere"] -w 0 ?h.inflated ?h.sphere||?h.sphere|| ||<rowbgcolor='#E0E0FF'>?h.sphere||["mris_register"] -w 0 -curv ?h.sphere $AvgTif ?h.sphere.reg||?h.sphere.reg|| ||<rowbgcolor='#E0E0FF'>rh.sphere||["mris_register"] -w 0 -curv -reverse rh.sphere $AvgTif rh.lh.sphere.reg||rh.lh.sphere.reg|| ||<rowbgcolor='#E0E0FF'>lh.sphere||["mris_register"] -w 0 -curv -reverse lh.sphere $AvgTif lh.rh.sphere.reg||lh.rh.sphere.reg|| ||<rowbgcolor='#E0E0FF'>?h.sphere.reg||["mrisp_paint"] -a 5 $AvgTif#6 ?h.sphere.reg ?h.avg_curv||?h.avg_curv|| ||<rowbgcolor='#E0E0FF'>?h.sphere.reg||["mris_ca_label"] -t $CPAnnotTable subj ?h sphere.reg $CPAtlas ?h.aparc.annot||label/?h.aparc.annot|| ||<rowbgcolor='#E0E0FF'>?h.aparc.annot||["mris_anatomical_stats"] -f scripts/?h.aparc.stats -b -a label/?h.aparc.annot subj ?h||scripts/?h.aparc.stats|| |
FreeSurfer Tutorial: Process Flow
recon-all step |
Input |
Command Line |
Output |
none |
file.dcm |
["mri_convert"] file.dcm orig/001.mgz |
orig/001.mgz |
["recon-all"] -autorecon1 -subjid subj |
|||
orig/001.mgz |
["mri_motion_correct2"] -i orig/001.mgz -i orig/002.mgz -o rawavg.mgz |
rawavg.mgz |
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orig/002.mgz |
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rawavg.mgz |
["mri_convert"] rawavg.mgz orig.mgz --conform |
orig.mgz |
|
orig.mgz |
["mri_convert"] orig.mgz orig.mnc |
orig.mnc |
|
orig.mnc |
(4 iterations of) ["nu_correct"] -clobber nu0.mnc nu1.mnc |
nu4.mnc |
|
nu4.mnc |
["mri_convert"] nu4.mnc nu.mgz |
nu.mgz |
|
nu.mgz |
["talairach2"] subjid -mgz |
transforms/talairach.xfm |
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nu.mgz |
["mri_normalize"] nu.mgz T1.mgz |
T1.mgz |
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T1.mgz |
["mri_watershed"] T1.mgz brain.mgz |
brain.mgz |
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Check skullstrip (brain.mgz), talairach (transforms/talairach.xfm), and normalization (brain.mgz or T1.mgz - mean wm voxel value = 110) |
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["recon-all"] -autorecon2 -subjid subj |
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brain.mgz |
["mri_em_register"] -mask brain.mgz -p .5 -fsamples fsamples.mgz nu.mgz $GCA transforms/talairach.lta |
transforms/talairach.lta |
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nu.mgz |
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brain.mgz |
["mri_ca_normalize"] -mask brain.mgz nu.mgz $GCA transforms/talairach.lta norm.mgz |
norm.mgz |
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nu.mgz |
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transforms/talairach.lta |
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brain.mgz |
["mri_ca_register"] -cross-sequence -mask brain.mgz -T transforms/talairach.lta norm.mgz $GCA transforms/talairach.m3z |
transforms/talairach.m3z |
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transforms/talairach.lta |
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norm.mgz |
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norm.mgz |
["mri_ca_label"] -cross-sequence norm.mgz transforms/talairach.m3z $GCA aseg.mgz |
aseg.mgz |
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transforms/talairach.m3z |
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brain.mgz |
["mri_normalize"] -mask brain.mgz nu.mgz T1.mgz |
T1.mgz |
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nu.mgz |
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T1.mgz |
["mri_mask"] T1.mgz brain.mgz brain.mgz |
brain.mgz |
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brain.mgz |
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brain.mgz |
["mri_segment"] brain.mgz wm.mgz |
wm.mgz |
|
wm.mgz |
["mri_edit_wm_with_aseg"] wm.mgz aseg.mgz wm.mgz |
wm.mgz |
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aseg.mgz |
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wm.mgz |
["mri_fill"] -a ../scripts/ponscc.cut.log -xform transforms/talairach.xfm -segmentation aseg.mgz wm.mgz filled.mgz |
filled.mgz |
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aseg.mgz |
../scripts/ponscc.cut.log |
||
filled.mgz |
["mri_tessellate"] filled.mgz 255 ../surf/lh.orig |
lh.orig |
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["mri_tessellate"] filled.mgz 128 ../surf/rh.orig |
rh.orig |
||
?h.orig |
["mris_smooth"] ?h.orig ?h.smoothwm |
?h.smoothwm |
|
?h.smoothwm |
["mris_inflate"] ?h.smoothwm ?h.inflated |
?h.inflated |
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?h.inflated |
["mris_sphere"] -w 0 -inflate -in 200 -q ?h.inflated ?h.qsphere |
?h.qsphere |
|
?h.qsphere |
["mris_fix_topology"] subj ?h |
?h.orig |
|
?h.orig |
["mris_euler_number"] ?h.orig |
?h.orig.euler |
|
?h.orig |
["mris_smooth"] ?h.orig ?h.smoothwm |
?h.smoothwm |
|
?h.smoothwm |
["mris_inflate"] ?h.smoothwm ?h.inflated |
?h.inflated |
|
brain.mgz |
["mris_make_surfaces"] -w 0 subj ?h |
?h.white |
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?h.orig |
?h.pial |
||
?h.thickness |
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orig.mgz |
["mri_surf2vol"] --mkmask --hemi ?h --fillribbon --template orig.mgz --volregidentity subj --outvol ?h.ribbon.mgz |
?h.ribbon.mgz |
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?h.white |
|||
?h.pial |
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Check final surfaces ["tkmedit]" subj wm.mgz ?h.white brain.mgz |
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["recon-all"] -autorecon3 -subjid subj |
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?h.inflated |
["mris_sphere"] -w 0 ?h.inflated ?h.sphere |
?h.sphere |
|
?h.sphere |
["mris_register"] -w 0 -curv ?h.sphere $AvgTif ?h.sphere.reg |
?h.sphere.reg |
|
rh.sphere |
["mris_register"] -w 0 -curv -reverse rh.sphere $AvgTif rh.lh.sphere.reg |
rh.lh.sphere.reg |
|
lh.sphere |
["mris_register"] -w 0 -curv -reverse lh.sphere $AvgTif lh.rh.sphere.reg |
lh.rh.sphere.reg |
|
?h.sphere.reg |
["mrisp_paint"] -a 5 $AvgTif#6 ?h.sphere.reg ?h.avg_curv |
?h.avg_curv |
|
?h.sphere.reg |
["mris_ca_label"] -t $CPAnnotTable subj ?h sphere.reg $CPAtlas ?h.aparc.annot |
label/?h.aparc.annot |
|
?h.aparc.annot |
["mris_anatomical_stats"] -f scripts/?h.aparc.stats -b -a label/?h.aparc.annot subj ?h |
scripts/?h.aparc.stats |