External Email - Use Caution Thanks Douglas. Unfortunately I am locked into using v5.3 as all of our previous images are processed with that version. Is there anything I can do within v5.3?
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 [ http://neura.edu.au/ | neura.edu.au ] [ https://twitter.com/neuraustralia | Twitter ] | [ https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ http://www.neura.edu.au/help-research/subscribe | Subscribe ] From: "Douglas N. Greve" <[email protected]> To: "Freesurfer support list" <[email protected]> Sent: Friday, 20 September, 2024 11:43:57 PM Subject: Re: [Freesurfer] Questions re Freesurfer editing 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: External Email - Use Caution Dear Mailing List, Can you please tell me how to address the following issues in Freesurfer version 5.3? 1. 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 [ http://neura.edu.au/ | neura.edu.au ] [ https://twitter.com/neuraustralia | Twitter ] | [ https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ http://www.neura.edu.au/help-research/subscribe | Subscribe ] _______________________________________________ Freesurfer mailing list [ mailto:[email protected] | [email protected] ] [ https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer | https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ] _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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