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

-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

orig.mgz

["mri_add_xform_to_header"] -c transforms/talairach.xfm orig.mgz orig.mgz

orig.mgz

-nuintensitycor

orig.mgz

["mri_nu_correct.mni"] --i orig.mgz --o nu.mgz --n 2

nu.mgz

-talairach

nu.mgz

["talairach_avi"] --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

transforms/talairach.xfm

["talairach_afd"] -T 0.005 -xfm transforms/talairach.xfm

transforms/talairach.xfm

awk -f $FREESURFER_HOME/bin/extract_talairach_avi_QA.awk transforms/talairach_avi.log

transforms/talairach_avi.log

-normalization

nu.mgz

["mri_normalize"] -g 1 nu.mgz T1.mgz

T1.mgz

-skullstrip

nu.mgz

["mri_em_register"] -skull nu.mgz $FREESURFER_HOME/average/RB_all_withskull_2007-08-08.gca transforms/talairach_with_skull.lta

transforms/talairach_with_skull.lta

T1.mgz

["mri_watershed"] -brain_atlas $FREESURFER_HOME/average/RB_all_withskull_2007-08-08.gca transforms/talairach_with_skull.lta -h 5 orig.mgz brainmask.auto.mgz

brainmask.auto.mgz

T1.mgz

["mri_mask"] T1.mgz brainmask.auto.mgz brainmask.auto.mgz

brainmask.mgz

brainmask.auto.mgz

cp brainmask.auto.mgz brainmask.mgz

brainmask.mgz

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

-gcareg

brainmask.mgz

["mri_em_register"] -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB_all_2007-08-08.gca transforms/talairach.lta

transforms/talairach.lta

nu.mgz

-canorm

brainmask.mgz

["mri_ca_normalize"] -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB_all_2007-08-08.gca transforms/talairach.lta norm.mgz

norm.mgz

nu.mgz

transforms/talairach.lta

-careg

brainmask.mgz

["mri_ca_register"] -align-after -nobigventricles -mask brainmask.mgz -T transforms/talairach.lta norm.mgz $FREESURFER_HOME/average/RB_all_2007-08-08.gca transforms/talairach.m3z

transforms/talairach.m3z

transforms/talairach.lta

norm.mgz

-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

transforms/talairach.m3z.inv.z.mgz

-rmneck

nu.mgz

["mri_remove_neck"] -radius 25 nu.mgz transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2007-08-08.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/RB_all_withskull_2007-08-08.gca transforms/talairach_with_skull.lta

transforms/talairach_with_skull.lta

nu_noneck.mgz

-calabel

norm.mgz

["mri_ca_label"] -align -nobigventricles norm.mgz transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2007-08-08.gca aseg.auto.mgz

aseg.auto.mgz

transforms/talairach.m3z

aseg.auto.mgz

cp aseg.auto.mgz aseg.mgz

aseg.mgz

-ccseg

aseg.mgz

["mri_cc"] -aseg aseg.auto.mgz -o aseg.auto_CCseg.mgz <subjid>

aseg.auto_CCseg.mgz

aseg.auto_CCseg.mgz

cp aseg.auto_CCseg.mgz aseg.mgz

aseg.mgz

-normalization2

brainmask.mgz

["mri_normalize"] -aseg aseg.mgz -mask brainmask.mgz -aseg aseg.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.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

aseg.mgz

brain.mgz

wm.asegedit.mgz

["mri_pretess"] wm.asegedit.mgz wm norm.mgz wm.mgz

wm.mgz

norm.mgz

-fill

wm.mgz

["mri_fill"] -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto.mgz wm.mgz filled.mgz

filled.mgz

aseg.mgz

../scripts/ponscc.cut.log

transforms/talairach.lta

-tessellate

filled.mgz

["mri_pretess"] ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz

norm.mgz

filled-pretess255.mgz

filled-pretess255.mgz

["mri_tessellate"] ../mri/filled-pretess255.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"] -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

-finalsurfs

brain.finalsurfs.mgz

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

?h.white

?h.pial

?h.thickness

?h.orig

?h.curv

?h.area, ?h.cortex.label

-smooth2

?h.white

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

?h.smoothwm

-inflate2

?h.white

["mris_inflate"] ?h.white ?h.inflated

?h.inflated

?h.sulc

-segstats

aseg.mgz

["mri_segstats"] --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --ctab $FREESURFER_HOME/ASegStatsLUT.txt --subject <subjid>

stats/aseg.stats

-cortribbon

orig.mgz

["mris_volmask"] --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance <subjid>

?h.ribbon.mgz

?h.white

?h.pial

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

-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

-jacobian_white

?h.white, ?h.sphere.reg

["mris_jacobian"] ../surf/?h.white ../surf/?h.sphere.reg ../surf/?h.jacobian_white

?h.jacobian_white

-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

aseg.mgz, ?h.sphere.reg

["mris_ca_label"] -aseg ../mri/aseg.mgz <subjid> ?h ../surf/?h.sphere.reg $FREESURFER_HOME/average/?h.curvature.buckner40.filled.desikan_killiany.gcs ../label/?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 label/aparc.annot.ctab

-cortparc2

aseg.mgz, ?h.sphere.reg

["mris_ca_label"] -aseg ../mri/aseg.mgz <subjid> ?h ../surf/?h.sphere.reg $FREESURFER_HOME/average/?h.atlas2005_simple.gcs ../label/?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 label/aparc.annot.a2005s.ctab subj ?h

stats/?h.aparc.a2005s.stats stats/aparc.annot.a2005s.ctab

-aparc2aseg

aseg.mgz

["mri_aparc2aseg"] --s subj --ribbon

aparc+aseg.mgz

?h.ribbon.mgz

label/?h.aparc.annot

-wmparc

aparc+aseg.mgz

["mri_aparc2aseg"] --s subj --labelwm --hypo-as-wm --rip-unknown --ribbon --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz

wmparc.mgz

wmparc.mgz

["mri_segstats"] --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject <subjid> --surf-wm-vol --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt

wmparc.stats