Hi Doug

I wanted to follow up this email and ask you a question. I see in the fspalm page, it says "You can use fspalm with both volume- and surface-based analyses; it will figure everything out". Considering your reply to the below email, I'm wondering if we can use fspalm for subcortical analysis or not?

I appreciate very much any comments on it.

Thanks Mona

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Monday, September 2, 2019 10:32 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] PALM Analysis

Sorry, fsplam is only for surfaces.

On 9/2/2019 7:46 PM, Harikumar, Amritha wrote:

Hi there,

I am trying to run a Permutation Analysis of Linear Models (PALM) for analyzing subcortical areas in the nucleus accumbens, caudate, and putamen. Upon trying to run the script after reading the Freesurfer wiki, I am not sure what it is referring to regarding applying fsPalm in MATLAB. My questions are - do we a.) copy paste the existing fspalm command in Matlab and run it after setting the two Freesurfer paths listed in the wiki, or what is the correct procedure to run it? I tried running it in terminal as well, but didn’t have any luck. My existing Matlab script has set up the two Freesurfer paths, and is trying to run the fsPalm command for each subcortical area of the three ROIs mentioned above, but that isn’t working either. Any help in running fsPalm would be greatly appreciated!

Thanks, Amritha

Amritha Harikumar Clinical Research Coordinator Holt Emotion and Social Neuroscience Lab Department of Psychiatric Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital ___________________________ 149 13th Street, Rm 2620A Charlestown, MA 02129 Phone: 617-724-3283

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