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README.md

MRI_tools

Matlab and Python tools for MRI analyses

Requirements

Python 3 (at least 3.6, but probably others) is required.

Python requirements are listed in the requirements.txt file, additionally pydeface version 2.0 is required to deface anatomical data (in prisma_to_BIDS.py; if either pydeface or FSL is unavailable, we will simply copy over the anatomical data), which also requires FSL, and the preprocessing script requires FSL (version 5.0.10, 6.0 doesn't seem to work) and Freesurfer.

For bidsGLM.m and its associated scripts, you will need GLMdenoise to run the GLM and, optionally, vistasoft if you want to run GLMdenoise on .mgz files (freesurfer surface files); for niftis, we use the built-in niftiread function.

How to use

Preprocessing

For an example of how to run, see the Winawer lab wiki

Prisma to BIDS

These functions can be used to transfer data from the default way it comes off NYU CBI's prisma scanner to a BIDS-compliant structure. This is only a temporary way of handling things, since eventually CBI will add BIDS as a possible export option. For an example of how to use this, see this script from the spatial frequency preferences experiment.

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Matlab and Python tools for MRI analyses

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