Installation

Just use pip

pip install vnav

parse_vNav_Motion.py

This is a small python script to parse the DICOM files from a vNavs series and convert them into an average RMS motion score. The script takes the following arguments:

1. --tr which is the TR of the parent sequence (i.e., the MPRAGE) expressed in seconds (e.g., --tr 2.4); and
2. --input which is the list of files DICOM files that makeup the vNavs series; or
3. --input-dir which is a directory containing DICOM files that makeup the vNavs series; or
4. --input-json which is a BIDS JSON sidecar file containing an ImageComments array; and
5. either --rms or --max which decides whether the time-averaged RMS motion or time-averaged max motion is printed; and
6. --output-dir which is the desired output directory

This script will output a JSON file containing

1. Transforms
2. HomogeneousTransforms
3. vNavMotionScoresRMS
4. vNavMotionScoresMax
5. MeanMotionScoreRMSPerMin
6. MeanMotionScoreMaxPerMin
7. Failed which is ether null or an array containing the AquisitionNumber and InstanceNumber where vNav failed.