Matlab and Python tools for MRI analyses
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.
For an example of how to run, see the Winawer lab wiki
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.