fMRI-preprocessing-SPM12

This is a SPM12 batch script that runs a standard fMRI preprocessing pipeline on a BIDS formatted data-set.

Included preprocessing steps

• defacing
• field map esimtation
• realignment and unwarping
• slice-time correction
• normalization
• smoothing

Requirements

• a BIDS formatted fMRI data-set See http://bids.neuroimaging.io/ for more information.
• a T1 anatomical image
• a field map
• at least 1 functional run (saved as a 4D nifti file) The scripts are written with the imaging sequences used at the GIfMI (http://gifmi.ugent.be/) in mind.

Bugs / Improvements

If you find bugs in this script or have suggestions for improvement, please report both here https://github.com/CCN-github/fMRI-preprocessing-SPM12/issues

Import raw data in the BIDS format

If you are interested in importing your data according to BIDS standards, go check out the scripts here https://github.com/NeuroStat/CustomFormatBIDS

Contact

[email protected]