Skip to content

FMRIPREP preprocessing

Jump to bottom
Sofia Fernandez edited this page Nov 15, 2019 · 5 revisions

Tutorial

How to run a minimal preprocessing pipeline and extract the nuissance confounds with FMRIRPREP in the LAVIS' ADA HPCC.

Requirements

Singularity image

In order to run 'fmriprep' inside ADA, a singularity image of 'fmriprep' must have been created and uploaded to an accessible location. For this tutorial, the path of the singularity image is: /mnt/MD1200B/egarza/sfernandezl/singimages/fmriprep20190725.img

BIDS

FMRIPREP requires that the input data are organized according to the BIDS standard. Even though 'fmriprep' comes with its own validator. It's recommended to run a BIDS validator separately before running the script.

Clone this wiki locally