bidsphysio

This is a modified version of bidsphysio package. The original package is accessible here.

Converts physio data (CMRR, AcqKnowledge, Siemens PMU) to BIDS physiological recording

Note: If desired, you can use the corresponding _bold.nii.gz BIDS file as --bidsprefix. The script will strip the _bold.nii.gz part from the filename and use what is left as <Prefix>. This way, you can assure that the output physiology files match the _bold.nii.gz file for which they are intended.

Installation

This is a modified version of the bidsphysio package.

You can install this version with pip:

mkdir /tmp/bidsphysio && \
    curl -sSL https://github.com/rezashr/bidsphysio/archive/master.tar.gz \
        | tar -vxz -C /tmp/bidsphysio --strip-components=1 && \
    cd /tmp/bidsphysio && \
    pip install . && \
    cd / && \
    rm -rf /tmp/bidsphysio

dcm2bidsphysio --infile <DCMfile> --bidsprefix <Prefix>
acq2bidsphysio --infile <acqfiles> --bidsprefix <Prefix>
pmu2bidsphysio --infile <pmufiles> --bidsprefix <Prefix> --dicom <DICOM DIR>
edf2bidsphysio --infile <edffile> --bidsprefix <Prefix>

Arguments

• <physiofiles> space-separated files with the physiological recordings.

  Supported file types:

  • <.dcm> or <.log>: DICOM or log file with physiological recording from a CMRR Multi-Band sequence (only a single file for <.dcm>).
  • <.acq>: AcqKnowledge file (BioPac).
  • <.puls> or <.resp>: Siemens PMU file (VB15A, VBX, VE11C).
  • <.edf> SR Research .edf file

• <Prefix> is the prefix that will be used for the BIDS physiology files. If all physiological recordings have the same sampling rate and starting time, the script will save the files: <Prefix>_physio.json and <Prefix>_physio.tsv.gz. If the physiological signals have different sampling rates and/or starting times, the script will save the files: <Prefix>_recording-<label>_physio.json and <Prefix>_recording-<label>_physio.tsv.gz, with the corresponding labels (e.g., cardiac, respiratory, etc.).

• <DICOM DIR> is the dicom directory of the functional images.

• --verbose will print out some warning messages.