fMRI EPI preprocessing pipeline which uses AFNI to compute and apply a set of transformations such that the EPI dataset ends up living in the space of a high-resolution anatomical dataset, The transformed dataset is then imported into a mrVistaSession which is ready to use with the vistalab vistasoft software. This package also contains novel existing code that was (slightly) modified to fit the current pipeline.
Existing codebase used in this project include:
r2aGUI (https://github.com/jeddobson/par_convert/blob/master/r2agui.m).
vistasoft (https://github.com/vistalab/vistasoft)
These functions were built to use AFNI version AFNI_19.0.21, and cannot be guaranteed to work with newer versions of AFNI.
Open EmptyStartfile.m, fill in the relevant fields and press play.
N.B. make sure that all data to be preprocessed contains AT LEAST the following components and follows the directory-tree structure specified below:
EPI-data, t1-matched data (t1 scanned in the same resolution/FOV/orientation as the EPI), and a high-resolution anatomical dataset that can be in any orientation.
ProjectDirectory/Participant/Session/datafiles_as_Stated_Above
Allows for participant and session batch processing if structured appropriately