Dear FreeSurfer community,

I am new to FreeSurfer and I apologize in advance if my questions are too naiive.

I have some nii files for both a localizer and an experiment. I would like to find some ROIs in the localizer, get their coordinates, create a mask, and then find those regions on the experiment data and run MVPA.

My main goal is to keep everything in the native space. Also, I am looking for percent signal change in selected ROIs.

Here is my approach to analyze the localizer data:

First, I ran the recon-all command. Then, I preprocessed the data in native space. The command that I ran was:

preproc-sess -s sess01 -fsd bold -stc odd -surface self lhrh -mni305 -fwhm 5 -per-session -force

Then, I configured my analyses and contrasts in each hemisphere, as well as the volume.

Finally, I ran the analyses for each hemispheres and the volume. I ran this command:

selxavg3-sess -s sess01 -analysis ffa.native.rh

Lastly, I visualized the results by running these commands:

tksurfer-sess -s sess01 -hemi rh -analysis ffa.native.rh -c faces-vs-bodies -self

tkmedit-sess -s sess01 -analysis ffa.native.mni -c faces-vs-bodies -self

So far, I think I have done everything correctly as am seeing the activation map where I am supposed to.

Now, I would like to be able to select some of these ROIs/clusters, take their voxel coordinates/numbers and create a mask. Then, use this mask on the main experiment (non localizer) nii files and get the signal value for only those voxels. Is this possible?

I have found this tutorial to create a functional ROI https://surfer.nmr.mgh.harvard.edu/fswiki/CreatingROIs but unfortunately I am not following it. I don't see these options in tksurfer.

Also is it possible to create an ROI on the surface?

I appreciate any help.

Thank you so much

Ashley Cole