fMRI-Tools

Miscellaneous general scripts for fMRI stuff.

renameDicomSeries

Takes as parameter the name of a directory containing sub-directories of DICOM files (each sub-directory representing the output of one series). Reads the 'SeriesDescription' field from the metadata of the first file in each sub-directory, copies contents of each sub-directory into new directory with the name of the series, and outputs a master log file with information about each series found.

mri_deface

CAUTION: de-facing using mri_deface is not clean, and may result in loss of brain data while maintaining identifiable face features.

Recommended to use Poldrack Lab's pydeface instead:

• pydeface - link to Poldrack Lab git repo
• Install FSL
• Run pip install nibabel nipype
• Clone above-linked git repo, run following:
  • cd pydeface
  • python setup.py install
• Takes NIfTI files as input, writes out NIfTI's with "_defaced" appended to filename

mri_deface usage, for reference

Copy of FreeSurfer's mri_deface tool for scan anonymization. Usage:

• mri_deface <input-file> <brain-template> <face_template> <output-file>
• Input file can be .mgz, .nii, or .dcm - if DICOM, only specify the first file in the series and the program will discover the rest.
• Works with NIfTI as output format, brain and face templates (talairach_mixed_with_skull.gca and face.gca) from FreeSurfer wiki page (see link above)