You probably want to mask the medial wall Bruce

On Dec 9, 2020, at 11:31 PM, Antonín Škoch ansk@ikem.cz wrote:



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Hi, Bruce,

in the meantime, I found the old thread

https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg05989.html

which suggests to set -N 20 parameter to mris_thickness to make thickness computation consistent to mris_make_surfaces. Indeed, the values are now consistent, with exception of several thousands of vertices mainly around medial wall. Is here any other option missing, which makes mris_thickness computed values of thickness fully consistent to mris_make_surfaces?

Thank you in advance,

Antonin

Hi, Bruce,

thank you for the instructions!

I ran mris_thickness on one example subject to test the procedure. However, inspecting the values of created thickness file, I encountered problem. In many locations, the values of thickness file differ from the values of thickness file created in recon-all -T2pial. Even when the input files used for thickness measurement are (should) be the same. (I double-checked my input surfaces, when I use woT2.pial surface, the thickness values are different everywhere).

Attached see the binarized difference of these thickness files with the cursor, where difference is zero (red spots) and where is non-zero (transparent).

Could you please clarify, where could be the problem? Does not the thickness computation in mris_make_surfaces use different options? Could it be the reason, that I am operating with data processed by longitudinal stream? (I don't think so...).

This inconsistence makes me puzzled.

Regards,

Antonin

Hi Antonín

You can specify what surfaces to use in mris_thickness:

mris_thickness -pial <path to pial surface> -white <path to white surface> …

cheers Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edumailto:freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edumailto:freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Antonín Škoch Sent: Wednesday, December 9, 2020 6:16 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Computing thickness from woT2.pial surfaces

External Email - Use Caution Dear experts,

I have processed my data with -T2pial option. I would like now to also compute thickness from woT2.pial surfaces (i.e. surfaces created by T1 only). Is here a comannd which does the trick, without running recon-all -pial (which rewrites current .pial and .thickness files generatedy by -T2pial? I am using freeSurfer version 6.0.

Thank you in advance,

Antonin Skoch

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