Hi,

I have a question about volume info from freesurfer vs matlab.

I am looking at, say, the left hippocampus volume from asegstats, which was 3778.2 mm^3.
When I try to get the same volume by loading aseg.nii on matlab, however, I get a different number, 3945.

For matlab, I used the following command, which counts the number of voxels equal to the left hippocampus segment id:
length(find(aseg.img==17))

This was done after I converted the original aseg.mgz file into native space, using 2 different methods:
(1) mri_convert -rl rawavg.mgz -rt nearest -i aseg.mgz -o bert_aseg.nii

(2) mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o bert_aseg.nii --regheader aseg.mgz
In both cases, the output was 3945.

The rawavg.mgz used here is also 1mm isovoxel, so I don't think it is due to the difference in voxel dimensions.

What could be the cause of the difference in volume?

Thanks,

Kristine

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