recon-all-dev step

Individual Flag

Input

Command Line

Output

["recon-all-dev"] -autorecon1 -subjid subj

-i <invol1> -i <invol2>

file1.dcm

["mri_convert"] file1.dcm orig/001.mgz

orig/001.mgz

file2.dcm

["mri_convert"] file2.dcm orig/002.mgz

orig/002.mgz

-motioncor

orig/001.mgz

["mri_motion_correct.fsl"] -o rawavg.mgz -wild orig/001.mgz orig/002.mgz

rawavg.mgz

orig/002.mgz

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"] T1.mgz brainmask.auto.mgz

brainmask.auto.mgz

brainmask.auto.mgz

cp brainmask.auto.mgz brainmask.mgz

brainmask.mgz

Check skullstrip (brain.mgz), talairach (transforms/talairach.xfm), and normalization (brain.mgz or T1.mgz - mean wm voxel value = 110)

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

-gcareg

brainmask.mgz

["mri_em_register"] -mask brainmask.mgz -p .5 nu.mgz $FREESURFER_HOME/average/RB40_talairach_2005-07-20.gca transforms/talairach.lta

transforms/talairach.lta

nu.mgz

-canorm

brainmask.mgz

["mri_ca_normalize"] -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB40_talairach_2005-07-20.gca transforms/talairach.lta norm.mgz

norm.mgz

nu.mgz

transforms/talairach.lta

-careg

brainmask.mgz

["mri_ca_register"] -align -mask brainmask.mgz -T transforms/talairach.lta norm.mgz $FREESURFER_HOME/average/RB40_talairach_2005-07-20.gca transforms/talairach.m3z

transforms/talairach.m3z

transforms/talairach.lta

norm.mgz

-rmneck

nu.mgz

["mri_remove_neck"] -radius 25 nu.mgz transforms/talairach.m3z $FREESURFER_HOME/average/RB40_talairach_2005-07-20.gca nu_noneck.mgz

nu_noneck.mgz

transforms/talairach.m3z

-skull-lta

transforms/talairach.lta

["mri_em_register"] -skull -t transforms/talairach.lta nu_noneck.mgz $FREESURFER_HOME/average/RB40_talairach_with_skull_2005-07-20.gca transforms/talairach_with_skull.lta

transforms/talairach_with_skull.lta

nu_noneck.mgz

-calabel

norm.mgz

["mri_ca_label"] -align norm.mgz transforms/talairach.m3z $FREESURFER_HOME/average/RB40_talairach_2005-07-20.gca aseg.auto.mgz

aseg.auto.mgz

transforms/talairach.m3z

aseg.auto.mgz

cp aseg.auto.mgz aseg.mgz

aseg.mgz

-segstats

aseg.mgz

["mri_segstats"] --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --in mri/orig.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 norm.mgz brain.mgz

brain.mgz

norm.mgz

brain.mgz

["mri_mask"] brain.mgz brainmask.mgz brain.finalsurfs.mgz

brain.finalsurfs.mgz

brainmask.mgz

-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

-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

transforms/talairach.lta

-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

-smooth1

?h.orig.nofix

["mris_smooth"] -nw ?h.orig.nofix ?h.smoothwm.nofix

?h.smoothwm.nofix

-inflate1

?h.smoothwm.nofix

["mris_inflate"] -dist 0 -no-save-sulc ?h.smoothwm.nofix ?h.inflated.nofix

?h.inflated.nofix

-qsphere

?h.inflated.nofix

["mris_sphere"] -w 0 -inflate -in 200 -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

-euler

?h.orig

["mris_euler_number"] ?h.orig

?h.orig.euler

-smooth2

?h.orig

["mris_smooth"] ?h.orig ?h.smoothwm

?h.smoothwm

-inflate2

?h.smoothwm

["mris_inflate"] -dist 0 ?h.smoothwm ?h.inflated

?h.inflated

?h.sulc

-finalsurfs

brain.finalsurfs.mgz

["mris_make_surfaces"] -mgz -w 0 -T1 brain.finalsurfs.mgz subj ?h

?h.white

?h.orig

?h.pial

?h.thickness

?h.curv

-cortribbon

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

-sphere

?h.inflated

["mris_sphere"] -w 0 ?h.inflated ?h.sphere

?h.sphere

-surfreg

?h.sphere

["mris_register"] -w 0 -curv ?h.sphere $AvgTif ?h.sphere.reg

?h.sphere.reg

-contrasurfreg

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

-avgcurv

?h.sphere.reg

["mrisp_paint"] -a 5 $AvgTif#6 ?h.sphere.reg ?h.avg_curv

?h.avg_curv

-cortparc

?h.sphere.reg

["mris_ca_label"] -t $CPAnnotTable subj ?h sphere.reg $CPAtlas ?h.aparc.annot

label/?h.aparc.annot

-parcstats

label/?h.aparc.annot

["mris_anatomical_stats"] -f scripts/?h.aparc.stats -b -a label/?h.aparc.annot subj ?h

stats/?h.aparc.stats