I'm not sure what to do about the medial surfaces. I don't think I've run into that problem before. For the other issue, those areas are the transverse sinus veins. In the next version, I have something that will segment those areas. You can get it now in the dev version. Then run mri_vsinus_seg --i orig.mgz --o vsinus.mgz You can then use vsinus.mgz to mask out the regions, eg, mri_mask -invert yourvolume.mgz vsinsus.mgz yourvolume-without-sinuses.mgz
On 9/20/2024 3:33 AM, Bronwyn Overs wrote:
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Dear Mailing List,
Can you please tell me how to address the following issues in Freesurfer version 5.3?
- Medial surface issues where the LH and RH Pial surfaces overlap
(indicated by orange circles in the attached 'medial_surface_issue.jpg'). Is this an issue that needs to be address, and if so, how is it done? 2. Regions of non-brain that have been labelled as cerebellum in the aseg file (indicated by the red circles in the attached image 'cerebellum_inclusions.jpg'). Can I rerun the skull stripping step or simply delete the erroneous voxels form the volume?
Kind regards,
Bronwyn Overs
Senior Research Assistant
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1725
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