Hi Rosalia,

The easiest way is probably to run mris_preproc, then feed the .mgz files thus generated directly into PALM, with design matrix and contrasts as you are already familiar with.

Also note that FreeSurfer now has a wrapper for PALM: http://freesurfer.net/fswiki/FsPalm

All the best,

Anderson

On 18 May 2018 at 15:35, Rosalia Dacosta Aguayo <[log in to unmask]> wrote:

---------- Forwarded message ----------
From: Rosalia Dacosta Aguayo <[log in to unmask]>
Date: 2018-05-18 2:53 GMT+02:00
Subject: Running statistics in FSL with Free Surfer outpouts
To: FSL - FMRIB's Software Library <[log in to unmask]>

Dear FSL experts,

I hope this is not a naive question and I can get some help from you.

I have run pre-processing with Free Surfer, but now that I  have to run the statistics, I would prefer to use your GLM as I have more experience with your software. The problem is that I do not know which of the outputs from Free Surfer (cortical thickness) I would have to use to run the statical comparisons. 

I would greatly appreciate if you could guide me on this.

Best regards,

Rosie

--

Rosalia Dacosta-Aguayo, PhD.

Rutgers University, Department of Physical Medicine and Rehabilitation.

Research Assistant Professor
Post Doctoral Fellow - Neuropsychology and Neuroscience / NNL Lab
Kessler Foundation
120 Eagle Rock Avenue, Suite 100
East Hanover, NJ 07936-3147
T. 973.323.3680  |  F. 973.386.1361 
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