External Email - Use Caution 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: > External Email - Use Caution > > 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 > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1pVHVj2Big8_HsyaQx4ad9XYI6M3HZhhYq23qZdpezzT0g88I_IXnFml_W7drewVjs0wi20gDUp2k3pPmxwsscuR_HokF601R8_ZCTTf4M3PFcc7IhBYYLhMLTCGJQ70maXEiPT5SwhemsxyOJIWo20cE_HG-yPlzUmbRiTKo9fpsErMXt-3-ezQhtDVOjibQA0NVwLpbsqkksvxGscQiRPFdeuBS6P0MNlDpqrZXMX0ncwG6sQxzGd457YcQFRI_wAK3UlHXDqYCYh3SOpkCsQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . 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.
