I am trying to derive wmparc volumes for a2009s which are by default not available in wmparc (segments read empty) _ is this because Desikan/Killiany atlas is used in wmparc by default?
So I decided to run
Mri_aparc2aseg for each subject using mri_aparc2aseg --s <subjid> --annot aparc.a2009s --o mri/wmparc.a2009.mgz --labelwm --rip-unknown --ctxseg aparc.a2009s+aseg.mgz
I thought this would generate a new wmparc which will now include labels for wm from a2009s
Then I ran
mri_segstats --seg mri/wmparc.a2009.mgz --sum stats/wmparc.a2009.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 MPRAGE04 --surf-wm-vol --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt
Hoping that this would allow me to obtain statistics from this wmparc file
But for some reason I am getting segmentation fault message as below
atlas_icv (eTIV) = 1663710 mm^3 (det: 1.170940 ) Loading mri/wmparc.a2009.mgz Getting Cerebral WM volumes from surface lh white matter volume 277542 rh white matter volume 284002 Loading mri/norm.mgz Loading mri/norm.mgz Loading mri/brainmask.mgz # nbrainmaskvoxels 1740943 # brainmaskvolume 1740943.0 # nbrainsegvoxels 260991 # brainsegvolume 260991.0 Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1190 segmentations Computing statistics for each segmentation 1 1 Left-Cerebral-Exterior 0 2 2 Left-Cerebral-White-Matter 0 3 3 Left-Cerebral-Cortex 0 4 4 Left-Lateral-Ventricle 3953 3953 5 5 Left-Inf-Lat-Vent 142 142 6 6 Left-Cerebellum-Exterior 0 7 7 Left-Cerebellum-White-Matter 15484 15484 8 8 Left-Cerebellum-Cortex Segmentation fault
Could anyone help please? Cheers Lena
_______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
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