I don't think the brain.mgz is the right one to look at as it has
already been partially segmented. Compare against the norm.mgz (or
nu.mgz) instead. It is really hard to determine where the lateral
boundaries are in thalamus
On 8/31/2022 2:46 AM, Thalhammer, Melissa wrote:
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Dear Freesurfers,
I have used the Freesurfer-based thalamus subnuclei segmentation. As a
quality control, we have inspected the output files visually in
freeview and noticed that some (roughly 5 out of 25 subjects) thalamic
volumes are (much) larger than the brain.mgz file would indicate (see
attached screenshot showing brain.mgz and
ThalamicNuclei.v12.T1.FSvoxelSpace.mgz). This seems to be the case for
aseg.mgz as well, i.e., the thalamus in aseg.mgz seems larger than it
should be based on the contrast we see in brain.mgz.
We have tried to run the segmentation again but this has not led to
significantly better results. Is this the right way to visualize the
outputs? Is it recommended to exclude these subjects? Is there any
recommended quality control pipeline that we could apply?
Thank you a lot in advance!
Best,
Melissa Thalhammer
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