Dear Doug/Bruce,

I appreciate any insights on this.

Thank you,

Ashely

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

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

First, I ran recon-all command. Then, I preprocessed the functional 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. I am seeing the activation ROIs where I am supposed to.

Now, I would like to be able to select these ROIs/clusters, take their voxel coordinates/numbers and create a mask. (These are my localizer nii files.) Then, use this mask on the main experiment (non localizer) nii files and get the percent signal change in those selected voxels. Is this possible?

I have found this tutorial 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