First, try running recon-all on the mni152 template Find the vertex closest to your seed coordinate You can create a circle on the surface with something like this (where vertexno is the vertex number you found above) mri_volsynth --dim nvertices 1 1 1 --pdf delta --delta-crsf vertexno 1 1 1 --o delta.mgz # create an overlay with all 0s except 1 at your target vertex mris_fwhm --so --niters 6 --i delta.mgz --o delta.sm6.mgz --s subject --hemi hemi  # Smooth it out to a radius of ABOUT 6mm mri_binarize --i delta.sm6.mgz --min 0.00000000000001 --o roi.mgz # Binarize it This should give you a circle with a radius of about 6mm. You can play with the --niters to make it bigger or smaller. You can then use mri_cor2label to convert this to a label, eg, mri_cor2label --i roi.mgz --id 1 --o roi.label --surf mni152recon lh You can then convert the label to an annotation with mris_label2annot

On 8/5/2021 4:59 AM, Paul Dhami wrote:

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Dear FS community,

My ultimate goal is to do a seed of interest connectivity analysis. Accordingly, I have MNI coordinates for a seed (e.g., left DLPFC). However, for the softwares I am using (CONN toolbox and Brainstorm), I need a .annot file which has the surface region of interest label I want to use as the seed.

My problem is I do not know how to create an .annot file from MNI coordinates of my seed/region of interest.

Can I create an .annot or label file with Freesurfer centered around an MNI coordinate, or would I first need to create a volume ROI using another software?

Any directions as to how I can do this would be greatly appreciated.

Best Wishes, Paul

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