Hi,

I suggest you start with the documentation that accompanies the recently released HCP pipelines.

see

http://www.humanconnectome.org/documentation/HCP-pipelines/

and the link therein to the pipelines on GitHub.

cheers,

-MH

Michael Harms, Ph.D.

-----------------------------------------------------------

Conte Center for the Neuroscience of Mental Disorders

Washington University School of Medicine

Department of Psychiatry, Box 8134

660 South Euclid Ave. Tel: 314-747-6173

St. Louis, MO 63110 Email: mharms@wustl.edu

From: Matthieu Vanhoutte <matthieuvanhoutte@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, September 19, 2014 9:23 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] HCP pipelines: fMRIVolume --> correction of gradient-nonlinearity-induced distortion

Dear Freesurfer's experts,

I'm trying to follow fMRI Volume pipeline from "The minimal preprocessing pipelines for the Human Connectome Project" (NeuroImage, 2013) on HCP data.

The first step has to be the correction of gradient-nonlinearity-induced distortion. The correction is then done with a customized version of the gradient_nonlin_unwarp package available in FreeSurfer (Jovicich et al., 2006).

I couldn't manage to find this package on internet, the only things I've found is the freesurfer grad_unwarp command and a webpage (https://surfer.nmr.mgh.harvard.edu/fswiki/GradientUnwarping) with no download link...

Where can I find this package and how to use it ?

Many thanks !

Best,

-------------------------------------
Matthieu Vanhoutte, MSc

Research Engineer - Department of Neuroradiology

Regional University Hospital, Lille, France