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If you download the dev version, you can run something like this: mri_binarize --dilate-vertex vtxno lh.white 10 lh.white.circle10.mgz where vtxno is the vertex no where you want the circle to be centered, 10 is the radius of the circle in mm It will not be a perfect circle as it is just adding vertices until the sum of the vertex areas reaches the desired circle area

On 5/4/2023 8:26 AM, Manenti, Giorgio wrote:

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Dear Experts,

My aim is to get circular ROIs. At the moment i am trying it on the flatmap, and i am writing a matlab script to do the task. However, I am getting a problem to open the output file (.flat) of the mris_flatten function as surface in MatLab.

I obtain the patch as "mris_flatten -w 0 -distances 20 7 lh.occip.patch.3d lh.occip.patch.flat “. The output is working properly on Freeview. However to make the circular ROIs pipeline faster and robust I would like to use Matlab. I tried to open the flattened patch via “read_curv”, “read_surf”,”read_patch” and also “MRIread” but all are returning the error “ could not open file ….” .

(i) Is there any suggestion to solve this issue? I would like to open the patch as i would do for a mask and afterwards create a circular ROI per each area of interest given the functional clusters (from sig.nii file) projected on the flatmap.

(ii) Is there any alternative to get circular ROIs on surface? Perhaps without GUI? For example via ‘mris_pmake’ ? Would i still require a flattened surface right?

Many thanks in advance Best

Giorgio

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