[Freesurfer] overlay activation map on flattened surface

External Email - Use Caution Hello Freesurfer team, I have flattened the occipital patch using "mris_flatten -w 10 subj04/surf/lh.occip.patch.3d subj04/surf/lh.occip.flattened" and it worked without any error and I can load the flattened patch in freeview. However, I have difficul

[Freesurfer] creating a cortical label using a 3D image ROI and calculating its volume and average thickness

External Email - Use Caution Dear Freesurfer users, I would like to do the following: - there is an ROI mask image file in the same space as the T1-weighted image - I would like to use that mask to define the borders of a cortical area - and then calculate volume and average t

[Freesurfer] Creating a custom registration template with FreeSurfer template

External Email - Use Caution Dear Freesurfer experts, I have issues with creating a custom registration template. (I'm following this instruction: https://secure-web.cisco.com/1_qfYxT5WNAR-lGRNh895Kl4pqE513hIRdGqZt0w-oDRR8NwLSUh8ataurmByizdN5-6NPpWldetuOVhBt0OSuQVw_fTGTUnlfnRy5

[Freesurfer] How to write rh.w-g.pct from recon-all stats output into a table

External Email - Use Caution I processed several items of data. And I have rh.w-g.pct file in my stats folders. How can I get process this file to get table reading file? I tried to use asegstats2table and aparcstats2table but it didn’t work. Could you provide me with necess