AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

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March 08, 2022 11:13AM
Thank you, Daniel!

I now understand better SUMA!

However, if I am not mistaken, 3dVol2Surf allows converting a volume in surface, if in the same space right?

My problem is that my atlases are in the subject space (to measure the surface of each individual).
Is there a way to apply the WARP (template to the subject) that I generated for each subject to the Charm surface atlas?

From what I understand, @animal_warper is generating surface files for atlases through the function atlas_followers, right?
If it is possible to do it with my WARP files, what would be the correct command line?

Finally, I read the doc of SurfaceMetrics and SurfMeasures I don't really get what would be the measure of surface: n_area_A? -area? (I am not sure what is the "area of each triangle")

There is another problem, which is that SurfMeasures is asking for a spec file, that I don't have since the subjects atlas are not generated with freesrufer (or others).

Using @animal_warper I have obtained a .gii file for the atlas with tcsh file
Since SurfaceMetrics doesn't seem to require a spec file, tried to measure the surface of a given ROI with the command:

SurfaceMetrics -area -i_gii native.k205.gii


However, I have got a file with 15425 rows, should I average all of them to have the total surface area of the ROI?
Finally, I guess that the next step to have the volume of each region, of a whole atlas is to repeat this command on all .gii of the atlas folder?

Thank you!
Subject Author Posted

Surface measures on CHARM

Doughboys February 23, 2022 03:48PM

Re: Surface measures on CHARM

Daniel Glen February 23, 2022 07:01PM

Re: Surface measures on CHARM

Doughboys March 08, 2022 11:13AM

Re: Surface measures on CHARM

Daniel Glen March 08, 2022 01:41PM

Re: Surface measures on CHARM

Doughboys March 18, 2022 03:36PM

Re: Surface measures on CHARM

Doughboys April 04, 2022 12:19PM

Re: Surface measures on CHARM

Daniel Glen April 04, 2022 01:16PM