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 >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
