Try using mri_label2vol instead of mri_convert. mri_convert just does a mapping whereas mri_label2vol knows that this is a segmentation doug
On 1/17/14 8:23 AM, Bruce Fischl wrote:
Hi Gabor
the volumes must change with reslicing. As to why they get consistently bigger in the hippocampus I'm not sure, probably something to do with its geometry
cheers Bruce On Fri, 17 Jan 2014, Gabor Perlaki wrote:
Dear all,
I've run the freesurfer on 3 subjects and converted the aseg.mgz into *.nii.gz in the native space:
"mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg2raw.nii.gz"
I've did a stats on left and right hippocampal volumes in the native space using fslstats:
"fslstats aseg2raw.nii.gz -l 16.5 -u 17.5 -V" for the left hippocampus
and
"fslstats aseg2raw.nii.gz -l 52.5 -u 53.5 -V" for the right hippocampus
The volumes given by fslstats was about 3% higher than the values reported in the aseg.stats file. The native resolution of the T1 images is 0.45*0.45*0.9 mm^3. I thought that observing a minimal difference could be the consequence of reslicing, but I really don't understand why fslstats gives consequently greater values (for both hippocampi in all three subjects).
Thanks, Gabor
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