Yes, looks like small registration errors. I don't think it is problematic. Any vertex where even a single subject has a 0 should be masked out of the final analysis.
On 12/3/2019 1:42 PM, Joëlle Ismay Rosanne Van Der Molen wrote: External Email - Use Caution Hi Douglas, Thank you for your quick response. Regarding the individual thickness mgh, it was a simple thresholding issue in the end (values were set to min 2), it looks now fine so this issue is resolved. About my initial first question concerning the presence of non-zero values in some areas where a majority of subjects have zeros, I computed the sum of subjects with a non-zero value per vertex and plotted this as an overlay in tksurfer, in order to better see the locations of these occurrences. (see files attached). I mainly see a small gradient around the medial temporal area. Could this indeed be due to small registration errors? Is this problematic? If yes, how to solve it? Thank you, Best regards, Joëlle ________________________________ De : freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu> de la part de Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu> Envoyé : mardi, 3 décembre 2019 02:14:08 À : firstname.lastname@example.org<mailto:email@example.com> Objet : Re: [Freesurfer] -qcache and thickness questions On 12/2/2019 7:12 PM, Joëlle Ismay Rosanne Van Der Molen wrote: External Email - Use Caution Dear Freesurfer experts, After running the -qcache option to extract thickness data for every subject, I tried pulling all the data together in order to get a matrix of subjects x vertices containing thickness data (for a given hemisphere) in all vertices of the brain. I noticed that for some small areas, particularly medial temporal, thickness data equals to 0 for some subjects, and has values for other subjects. May this be of concern? If so, would you have any idea why this is happening? It is hard to say without seeing the locations. There are sometimes places on the edge of the medial wall where there are some small errors in registration and so things don't line up perfectly. Could that be it? Another, perhaps related question is: when I try to use a subject's individual thickness mgh as an overlay in tksurfer, I obtain the outputs attached to this email (I am not modifying any overlay min max or threshold values). I am wondering if these grey zones in the map (around occipital and parietal areas specifically; not for subcortical areas) are to be expected, or if they may reflect some processing problem? If so, what problem could it be? I would say that those images look problematic. Is that the individual's surface or is it after mapping to fsaverage? In any event, you should look at the surfaces overlaid on the volume to see if the thickness is 0. Thank you in advance for your help, Best regards, Joëlle van der Molen _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ 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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