Recon-all steps and stages
recon-all step |
Individual Flag |
Input |
Command Line |
Output |
none |
none |
file.dcm |
["mri_convert"] file.dcm orig/001.mgz |
orig/001.mgz |
["recon-all"] -autorecon1 -subjid subj |
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-motioncor |
orig/001.mgz |
["mri_motion_correct2"] -i orig/001.mgz -i orig/002.mgz -o rawavg.mgz |
rawavg.mgz |
|
orig/002.mgz |
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rawavg.mgz |
["mri_convert"] rawavg.mgz orig.mgz --conform |
orig.mgz |
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-nuintensitycor |
orig.mgz |
["mri_convert"] orig.mgz orig.mnc |
orig.mnc |
|
orig.mnc |
(4 iterations of) ["nu_correct"] -clobber nu0.mnc nu1.mnc |
nu4.mnc |
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nu4.mnc |
["mri_convert"] nu4.mnc nu.mgz |
nu.mgz |
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-talairach |
nu.mgz |
["talairach2"] subjid -mgz |
transforms/talairach.xfm |
|
-normalization |
nu.mgz |
["mri_normalize"] nu.mgz T1.mgz |
T1.mgz |
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-skullstrip |
T1.mgz |
["mri_watershed"] T1.mgz brain.mgz |
brain.mgz |
|
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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-cgareg |
brain.mgz |
["mri_em_register"] -mask brain.mgz -p .5 -fsamples fsamples.mgz nu.mgz $GCA transforms/talairach.lta |
transforms/talairach.lta |
|
nu.mgz |
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-canorm |
brain.mgz |
["mri_ca_normalize"] -mask brain.mgz nu.mgz $GCA transforms/talairach.lta norm.mgz |
norm.mgz |
|
nu.mgz |
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transforms/talairach.lta |
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-careg |
brain.mgz |
["mri_ca_register"] -cross-sequence -mask brain.mgz -T transforms/talairach.lta norm.mgz $GCA transforms/talairach.m3z |
transforms/talairach.m3z |
|
transforms/talairach.lta |
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norm.mgz |
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-calabel |
norm.mgz |
["mri_ca_label"] -cross-sequence norm.mgz transforms/talairach.m3z $GCA aseg.mgz |
aseg.mgz |
|
transforms/talairach.m3z |
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-normalization2 |
brain.mgz |
["mri_normalize"] -mask brain.mgz nu.mgz T1.mgz |
T1.mgz |
|
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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-segmentation |
brain.mgz |
["mri_segment"] brain.mgz wm.mgz |
wm.mgz |
|
-edit_wm_with_aseg |
wm.mgz |
["mri_edit_wm_with_aseg"] wm.mgz aseg.mgz wm.mgz |
wm.mgz |
|
aseg.mgz |
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-fill |
wm.mgz |
["mri_fill"] -a ../scripts/ponscc.cut.log -xform transforms/talairach.xfm -segmentation aseg.mgz wm.mgz filled.mgz |
filled.mgz |
|
aseg.mgz |
../scripts/ponscc.cut.log |
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-tessellate |
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 |
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-smooth1 |
?h.orig |
["mris_smooth"] ?h.orig ?h.smoothwm |
?h.smoothwm |
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-inflate1 |
?h.smoothwm |
["mris_inflate"] ?h.smoothwm ?h.inflated |
?h.inflated |
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-qsphere |
?h.inflated |
["mris_sphere"] -w 0 -inflate -in 200 -q ?h.inflated ?h.qsphere |
?h.qsphere |
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-fix |
?h.qsphere |
["mris_fix_topology"] subj ?h |
?h.orig |
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-euler |
?h.orig |
["mris_euler_number"] ?h.orig |
?h.orig.euler |
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-smooth2 |
?h.orig |
["mris_smooth"] ?h.orig ?h.smoothwm |
?h.smoothwm |
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-inflate2 |
?h.smoothwm |
["mris_inflate"] ?h.smoothwm ?h.inflated |
?h.inflated |
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-finalsurfs |
brain.mgz |
["mris_make_surfaces"] -w 0 subj ?h |
?h.white |
|
?h.orig |
?h.pial |
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?h.thickness |
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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 |
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?h.white |
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?h.pial |
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Check final surfaces ["tkmedit"] subj wm.mgz ?h.white -aux 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 |
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?h.sphere |
["mris_register"] -w 0 -curv ?h.sphere $AvgTif ?h.sphere.reg |
?h.sphere.reg |
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rh.sphere |
["mris_register"] -w 0 -curv -reverse rh.sphere $AvgTif rh.lh.sphere.reg |
rh.lh.sphere.reg |
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lh.sphere |
["mris_register"] -w 0 -curv -reverse lh.sphere $AvgTif lh.rh.sphere.reg |
lh.rh.sphere.reg |
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?h.sphere.reg |
["mrisp_paint"] -a 5 $AvgTif#6 ?h.sphere.reg ?h.avg_curv |
?h.avg_curv |
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?h.sphere.reg |
["mris_ca_label"] -t $CPAnnotTable subj ?h sphere.reg $CPAtlas ?h.aparc.annot |
label/?h.aparc.annot |
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?h.aparc.annot |
["mris_anatomical_stats"] -f scripts/?h.aparc.stats -b -a label/?h.aparc.annot subj ?h |
scripts/?h.aparc.stats |