flywheel/bxh-xcede-tools-qa

Build context for a Flywheel Gear to execute bxh-xcede-tools QA using fmriqa_generate.pl and fmriqa_phantomqa.pl.

Description

These tools perform QA (quality assurance) calculations and produce images, graphs, and/or XML data as output. fmriqa_phantomqa.pl and fmriqa_generate.pl produce an HTML report with various QA measures. fmriqa_phantomqa.pl was designed for fMRI images of the BIRN stability phantom, and fmriqa_generate.pl has been used for human fMRI data.

Build the Image

To build the image, either download the files from this repo or clone the repo:

docker build --no-cache -t flywheel/bxh-xcede-tools-qa

Inputs

The input to this gear can be either a zip, a tgz, or a directory containing DICOMs.

Outputs

A summary HTML file is the sole output of this gear - prefixed with the name of the input DICOM archive, like so:

output_html_file="${OUTPUT_DIR}"/`basename "$dicom_input"`_fmriqa.qa.html

Options

Default options are set in manifest.json and copied to the container on build. Defaults are then loaded by the run script when the algorithm is executed.

Example Docker Usage

While this Gear is meant for execution within a Flywheel instance, you can run it locally with the following command.

# Be sure the input file (DICOM archive or files) resides in ./input/fmri_dicom_input/:
docker run -ti --rm \
      -v `pwd`/input:/flywheel/v0/input \
      -v `pwd`/output:/flywheel/v0/output \
      flywheel/bxh-xcede-tools-qa