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||<|2(bgcolor='#FFFFE0'>-motioncor||<bgcolor='#E0E0FF'>orig/001.mgz||<|2(bgcolor='#E0E0FF'>["mri_motion_correct2"] -i orig/001.mgz -i orig/002.mgz -o rawavg.mgz||<|2(bgcolor='#E0E0FF'>rawavg.mgz|| ||<|3(bgcolor='#FFFFE0'>-motioncor||<bgcolor='#E0E0FF'>orig/001.mgz||<|2(bgcolor='#E0E0FF'>["mri_motion_correct2"] -i orig/001.mgz -i orig/002.mgz -o rawavg.mgz||<|2(bgcolor='#E0E0FF'>rawavg.mgz||
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||<rowbgcolor='#E0E0FF'>rawavg.mgz||["mri_convert"] rawavg.mgz orig.mgz --conform||orig.mgz||
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||<rowbgcolor='#E0E0FF'>rawavg.mgz||["mri_convert"] rawavg.mgz orig.mgz --conform||orig.mgz||

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

-motioncor

orig/001.mgz

["mri_motion_correct2"] -i orig/001.mgz -i orig/002.mgz -o rawavg.mgz

rawavg.mgz

orig/002.mgz

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

nu.mgz

["mri_normalize"] nu.mgz T1.mgz

T1.mgz

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)

["recon-all"] -autorecon2 -subjid subj

brain.mgz

["mri_em_register"] -mask brain.mgz -p .5 -fsamples fsamples.mgz nu.mgz $GCA transforms/talairach.lta

transforms/talairach.lta

nu.mgz

brain.mgz

["mri_ca_normalize"] -mask brain.mgz nu.mgz $GCA transforms/talairach.lta norm.mgz

norm.mgz

nu.mgz

transforms/talairach.lta

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

norm.mgz

norm.mgz

["mri_ca_label"] -cross-sequence norm.mgz transforms/talairach.m3z $GCA aseg.mgz

aseg.mgz

transforms/talairach.m3z

brain.mgz

["mri_normalize"] -mask brain.mgz nu.mgz T1.mgz

T1.mgz

nu.mgz

T1.mgz

["mri_mask"] T1.mgz brain.mgz brain.mgz

brain.mgz

brain.mgz

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

aseg.mgz

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

filled.mgz

["mri_tessellate"] filled.mgz 255 ../surf/lh.orig

lh.orig

["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

?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

?h.orig

?h.pial

?h.thickness

orig.mgz

["mri_surf2vol"] --mkmask --hemi ?h --fillribbon --template orig.mgz --volregidentity subj --outvol ?h.ribbon.mgz

?h.ribbon.mgz

?h.white

?h.pial

Check final surfaces ["tkmedit]" subj wm.mgz ?h.white brain.mgz

["recon-all"] -autorecon3 -subjid subj

?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

ReconAllTable (last edited 2017-10-24 13:48:37 by MorganFogarty)