Adapted from: Hocke, & Fredrick. (2020). Post‐hoc physiological waveform extraction from motion estimation in simultaneous multislice (SMS) functional MRI using separate stack processing
BreathLess is a script to extract a predicted respiratory waveform from fMRI data. The script takes an fMRI image in BIDS format with the proper json sidecar. If you do not have this, I suggest subclassing the BidsImg class to trick the Breathless script into thinking the file is in proper bids format.
- System requirements - 3dvolreg
- Python requirements - in requirements.txt
-
Install dependencies with
pip install -r requirements -
Run script with
python breathless/breathless.py <name_of_bids_file>
Requirements:
* Data must be in BIDS format
* Data must have BIDS json sidecar containing: SliceTiming, RepetitionTime, PhaseEncodingDirection