/estimate_respiratory_traces

Primary LanguageJupyter Notebook

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.

Instructions

  • System requirements - 3dvolreg
  • Python requirements - in requirements.txt

  1. Install dependencies with pip install -r requirements

  2. 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