External Email - Use Caution Thanks, Niels. It is definitely a matter of hyperintensity of voxels close to the lateral boundary, particularly in the anterior region (which has a fuzzy boundary with the white matter in first place). Whether these hyperintensities are due to MS pathology, that I do not know (I’m really not the person to tell…). These could be cleaned up with postprocessing (e.g., filling holes, or using a Markov Random Field), but the impact on the volumes would be negligible. 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: Niels Bergsland <theni...@gmail.com> Date: Wednesday, 10 October 2018 at 15:42 To: "Iglesias Gonzalez, Eugenio" <e.igles...@ucl.ac.uk> Subject: Re: [Freesurfer] Disjointed thalamic nuclei segmentation Hi Eugenio, Thanks for the lightning fast response! :) I've attached them here. It looks like it might actually be the opposite in this case in that the voxels here are darker. Some of the cases are MS patients and so it's conceivable that they have thalamic lesions. Admittedly though, I have not really spent time in the past looking for thalamic lesions on T1-weighted images and this hasn't been an issue in the past since the thalamic segmentation in the aseg doesn't end up being affected by these voxels with lower intensities. If you would like to look at some other cases or need other outputs, just let me know and I'm happy to send them along! Thanks again, Niels On Wed, Oct 10, 2018 at 4:30 PM Iglesias Gonzalez, Eugenio <e.igles...@ucl.ac.uk<mailto:e.igles...@ucl.ac.uk>> wrote: External Email - Use Caution 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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Niels Bergsland <theni...@gmail.com<mailto:theni...@gmail.com>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Wednesday, 10 October 2018 at 15:22 To: Freesurfer Mailing List <freesurfer@nmr.mgh.harvard.edu<mailto: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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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