External Email - Use Caution It's solved. I understood the problem. I masked the volume to extract the hemisphere and within this masked volume I Iabeled pial matter. Therefore when creating surfaces, I saw the outer-most part of this label. But then I labeled all the "empty" parts outside the masked volume as "pial matter". So I got the surface I was looking for.
I think labeling in T2 images also factored in this issue because inT1 images outside the brain and pial- both are completely black. But anyways, this was not freesurfer technical problem. Thanks anyways, with reegards, malav From: "Wang, Ruopeng" <rwa...@mgh.harvard.edu> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Wednesday, June 14, 2023 11:54:58 PM Subject: Re: [Freesurfer] place pial matter on top of the cortex using segmentation volume External Email - Use Caution Why can’t you visualize it on the pial surface? Any error message when you attempt to do that? Can you elaborate? On Jun 14, 2023, at 12:12 PM, Malav Shah < [ mailto:malav.s...@bccn-berlin.de | malav.s...@bccn-berlin.de ] > wrote: External Email - Use Caution Thanks for your reply, Wang. Sorry if the question was not clear. I will try to elaborate better. Here is a cropped image from the previous screenshot. This is a T2 sequence, and with a manipulated contrast, so the overall brightness is very high. <pial_matter_blancket.png> I segmented the elephant brain MRI into grey-, pial-, and white-matter. Using 'mri_tesselate' command, I got GM-WM boundaries (yellow surface) and GM-pial matter boundary (red surface). Then, I got cortical thickness as distance b/w these surfaces, using mri_diff command, and I can visualise this on GM-WM (yellow) surface (at the green arrow). However, I want to visualize this on the red surface (where the pink arrow is), but I can't. The closest is, I can see this on the most outer pial surface (where the blue arrow is), and as that is purely noise (which makes sense) and not even useful visualisation. In essence, the most useful information for me is at GM-pial boundary (the pink arrow)- for inflating, measuring curvature, or surface area or visualising the cortical thickneess. I hope this clarifies the problem. Thanks in advance. with regards, malav From: "Wang, Ruopeng" < [ mailto:rwa...@mgh.harvard.edu | rwa...@mgh.harvard.edu ] > To: "Freesurfer support list" < [ mailto:freesurfer@nmr.mgh.harvard.edu | freesurfer@nmr.mgh.harvard.edu ] > Sent: Wednesday, June 14, 2023 4:47:08 PM Subject: Re: [Freesurfer] place pial matter on top of the cortex using segmentation volume External Email - Use Caution I’m not sure if I understood what you are trying to show. If you want to show the cortical thickness on top of the pial surface, you can load it as an overlay. Ruopeng BQ_BEGIN On Jun 14, 2023, at 7:30 AM, Malav Shah < [ mailto:malav.s...@bccn-berlin.de | malav.s...@bccn-berlin.de ] > wrote: External Email - Use Caution Dear freeesurfer team, Thank you for your support. I have cortical thickness measurements. I want to know if I can visualise it on top of the pial matter surface. I guess my mail missed the thread conversation, so asking as a new issue. At the moment, I can see only white matter surface in its appropriate form. Pial surface looks more like a blanket on top of the grey matter, rather than bedsheet as it should ideally look. I understand that's the issue because Iextract pial matter with mri_tesselate command from tissue segmentation (white-, pial- and grey-matter labels). I think I am looking for pial matter surface that the command 'mris_place_surface' generates in traditional recon-all pipeline, and want to measure its curvature and surface area). Can you please suggest how can use that command, or some other alternate to see pial mattter on top of the cortex? Thank you in advance. - malav <pial_matter_blancket.png> Malav Shah PhD candidate, Michael Brecht Lab, Humboldt University zu Berlin. 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