Hello Freesurfers, I have been using mri_compute_volume_fractions for a while and I just noticed something weird. Some clearly csf pixels (sometime very large groups) are not filled in the *.csf.mgz image mri_compute_volume_fractions produces The first following figure shows a posterior coronal slice, with the csf image overlaid with heat colormap. Look at the curser in the left calcarine sulcus for an obvious example, and note that it is not due to some particular slice cut. [cid:image002.png@01D0E413.F57966B0]
These voxels are instead wrongly assigned to gray matter by mri_compute_volume_fractions, as can be seen in the *.gm.mgz image below (same slice). [cid:image006.png@01D0E413.F57966B0] Seems like at least this particular spot of the volume is handled ok by other parts of freesurfer's pipeline since the cortical ribbon */mri/ribbon.mgz does not include it (does not consider it to be gray or white matter; figure below) [cid:image008.png@01D0E413.F57966B0] You can understand that this worries me a bit. I found $FREESURFER_HOME/VERSION file, which tells me I am running the following Freesurfer version: freesurfer-x86_64-unknown-linux-gnu-stable5-20130513 I am running Ubuntu 14.04.3 LTS on a 64-bit machine. Thanks a lot for any help! Sébastien Proulx
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