What is CMRIF_preprocess?

This program is a centralized hub for all your MRI preprocessing needs. It has three main features: A disk image optimized for MRI computation, a script that takes DICOM or NIFTI images and organizes them into BIDS standard formatting, and finally a modular preprocessing script that uses nipype to allow you to mix and match different preprocessing packages from different software (such as using BET from FSL and AFNI's anat2epi).

To get started, get an AWS account and go to our getting started page.

Disk Image Includes

Software: Afni, Freesurfer, Fsl, Anaconda (python 3.7)

Python packages: boto3, pathlib, pybids, pydicom, nipype, pip, tedana

Ubuntu packages: dcm2niix, pigz

Host Requirements

Linux:

xauth

Mac:

xQuartz