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.
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" RWANG4@MGH.HARVARD.EDU To: "Freesurfer support list" 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
On Jun 14, 2023, at 7:30 AM, Malav Shah < [ mailto:malav.shah@bccn-berlin.de | malav.shah@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. (+49) 163-216-9391 _______________________________________________ Freesurfer mailing list [ mailto:Freesurfer@nmr.mgh.harvard.edu | Freesurfer@nmr.mgh.harvard.edu ] https://secure-web.cisco.com/1Oxx33nDO9jKyGYqQpRpjDiKvHSK6TtsaHq1DWlFdm38W-_...
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1Oxx33nDO9jKyGYqQpRpjDiKvHSK6TtsaHq1DWlFdm38W-_... 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://secure-web.cisco.com/1dwMB55-WKmzVU0NvWTKgXLlof6rDrxVuLKKnUFti7Eig20... https://secure-web.cisco.com/1dwMB55-WKmzVU0NvWTKgXLlof6rDrxVuLKKnUFti7Eig20xyHlbKbFrArTVUFXQ1DkQ2fIEDWMmDUDoYNzBriC6mLgBzLPvJl5LRLvvF2UYGPmnXYKTogmxOtXGO1O_nnfN9iIfe6yEmmTmQvRs9aiE3jXTp53XYtSIVsLctrWoGKwiUbjxMR81nVD_vsJXSBR2mfb9xlXn5V0ZxI-VFC0qZfl4ATf1Pp-G_QJtwSLL3ElL7ElWsfACVE3jq3KV86bClUG66q3VarfrWYV0gCkGyVDBFJXPbbLO8yE72dyub7O8dpoCDo7FesAnTbL2DlRZCAGcAdkLGzrws6atwtw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . 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.
