You should be able to do it that way. When you run mkanalysis, specify -funcstem fmcpr.sm0.fsaverage.lh.nii.gz, and then selxavg3-sess will then use that file as input. If you want to smooth, then do that explicitly and pass the smoothed file to mkanalysis

On 04/06/2017 12:35 PM, Christopher Markiewicz wrote:

Hi list,

We're working on making a preprocessing stream that will be generally accessible to different analysis streams, including FreeSurfer. One component of this is sampling functional volumes to FreeSurfer meshes, and I want to test this component by running a simple first-level GLM in FreeSurfer.

I've always done this through the FSFAST pipeline, but that may be a bit much, given that I'm starting from surface time series (the equivalent of `$FUNCTIONALS_DIR/$SESS_ID/bold/$RUN/fmcpr.sm0.fsaverage.lh.nii.gz`, but as a GIFTI file).

Supposing I have a paradigm file and the files described above, what's the best way to do a basic GLM? Would it be to `mri_surf2surf` our GIFTI surfaces into `fmcpr.sm0.fsaverage.lh.nii.gz` files in a FSFAST directory structure, and pick up at `mkanalysis-sess`? Or is there a more straightforward way to just get a simple set of contrasts to compare with a volumetric analysis?

Thanks in advance, Chris Markiewicz

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