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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