Dear Franciska, It’s hard to tell from a single plane, but it seems that dark voxels from the ventricles are mixing with bright voxels from the corpus callosum, into gray voxels looking like the pulvinar and medical nuclei. Would you be able to share the whole subject so I can take a closer look? Cheers, /E
Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Gronow, Franziska" <franziska.gro...@uniklinikum-dresden.de> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, February 17, 2021 at 03:54 To: "'freesurfer@nmr.mgh.harvard.edu'" <freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation? External Email - Use Caution Dear Freesurfer experts, I’ve been using Freesurfer 7 for only a few months. I've searched the list and no similar observations have been reported. For my project I used the „Segmentation of thalamic nuclei“ tool by Iglesias, J.E. et al. The „recon-all“ as well as the thalamic segmentation process have been run. For quality control an outlier script was used to identify statistical outliers. In the course of the visual QC the PuM nucleus appeared to be mis-segmented in many cases – regardless of whether it was flagged as statistical outlier or not. I was wondering whether others had similar experiences and whether there are any recommendations how to handle such cases. We thought about excluding this area from our analysis for all subjects. Would you recommend such a procedure? I uploaded on dropbox 3 screenshots of a typical case (with/without/low opacity mask) so that you get an idea of what I mean: https://www.dropbox.com/sh/53fhanytrt4es6e/AAAqEmgl7N5YqpxDYMfxHQDAa?dl=0 Thanks for your help! Best, Franziska
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