You will need a registration between the space where the ROIs are and the anatomical. We usually do this with bbregister, but you will need to identify a volume that is in the ROI space that has anatomical contrast so that the registration can be done (ie, dont use the ROI mask for registration). Then you can run mri_vol2surf specifying the ROI.nii.gz as the mov volume and the registration from bbregister. After that you should just be able load it as an overlay on the patch.

On 12/9/16 6:44 AM, Niia Nikolova wrote:

Dear Experts,

I have analysed retinotopy data, and have it on occipital patches of each subjects cortical flatmap. Now, I would like to also project ROI masks which I have drawn by hand in FSL (based on other functional areas) onto the same flatmaps. The ROI masks are in 3d nii.gz files and I am not sure how to approach this.

I have followed the freesurfer tutorials and searched in the mail archives, but have not encountered a similar problem. If you could point me in the right direction, I would greatly appreciate it!

Thank you in advance, Niia _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer