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:

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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  

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