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Thanks, Niels. I suspect the problem is that, for some reason, such voxels have much brighter intensity than their surroundings, and are classified as white matter / reticular nucleus. But that shouldn’t be happening that far from the lateral boundary of the thalamus… Can you please send us norm.mgz and the thalamic segmentation file, so I can take a look? Cheers, /Eugenio
-- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Niels Bergsland theniels@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Wednesday, 10 October 2018 at 15:22 To: Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Disjointed thalamic nuclei segmentation
External Email - Use Caution Hi Eugenio, Thank you again for the fantastic thalamic nuclei segmentation tool!
I'm going through and QC'ing a batch of subjects that were processed through the pipeline. Data was originally processed with freesurfer-6.0.0 and then processed through the thalamic nuclei stream (dev-20180818-e30e6f9).
I have found that for some cases, there are some isolated patches of voxels that are disconnected and seemingly in the wrong place. I've noticed it primarily for the MDm and my impression is that it tends to happen more in the right hemisphere. I've attached a sample image to show you what I mean. The red cross has been placed on a set of these voxels. It is not the case that they are connected in 3D.
Any input is appreciated and thanks again! If it can be useful, I'm happy to upload the data
-Niels