Hi Doug,
Thanks for your reply. However, I was not able to succeed. Can you give me an extra help? I created a new color table and I tried the following command:
mri_segstats --seg $SUBJECTS_DIR/Subjid/mri/lobe+aseg.mgz --pv $SUBJECTS_DIR/Subjid/mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask $SUBJECTS_DIR/Subjid/mri/brainmask.mgz --in $SUBJECTS_DIR/Subjid/mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject Subjid --surf-wm-vol --ctab $FREESURFER_HOME/FreeSurferColorLUT_lobe.txt --sum Subjid.aseg.sum
But it only makes calculations for temporal and parietal lobes and they don't seem like valid numbers.
This is what is shown in the command line:
Loading /home/user/Projects/Freesurfer/AC/mri/lobe+aseg.mgz Getting Cerebral WM volumes from surface lh white matter volume 224173 rh white matter volume 229757 Loading /home/user/Projects/Freesurfer/AC/mri/norm.mgz Loading /home/user/Projects/Freesurfer/AC/mri/norm.mgz Loading /home/user/Projects/Freesurfer/AC/mri/brainmask.mgz # nbrainmaskvoxels 1506513 # brainmaskvolume 1506513.0 # nbrainsegvoxels 232396 # brainsegvolume 232396.0 Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 7 segmentations Computing statistics for each segmentation 1 1 frontal 0 2 2 cingulate 0 3 3 occipital 0 4 4 temporal 3706 3706 5 5 parietal 247 247 6 6 insula 0
Reporting on 2 segmentations
Hope you can help. Thank you very much,
ines
On Mon, Apr 2, 2012 at 6:38 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
use mri_segstats. You can look in subjid/scripts/recon-all.log for example command lines (look for the one with wmparc). The command will require a color table. The ones in the log file will use the default table, but this will not have the numbers/names of your lobar regions, so you'll need to create a new color table (or add to the one that is there). doug
On 04/02/2012 12:58 PM, Inês Violante wrote:
Dear all,
I need to obtain the white matter volume per lobe for a given numer of subjects. I started by using the following:
mri_annotation2label --subject<subjid> --hemi rh --lobesStrict lobe
mri_aparc2aseg --s<subjid> --labelwm --annot lobe
and now I have a lobe+aseg.mgz file. How can I create a stats file containing the wm volume for each lobe?
Thank you,
ines
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