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Create graphical reports for the MRIQC image quality metrics.

License: Apache License 2.0

Python 91.93% Dockerfile 0.40% Makefile 1.76% CSS 0.31% Shell 5.59%

qmtools's Introduction

QMTools - Quality Metrics Tools

This is a public code repository of the Translational Bioimaging Resource–MRI core group at the University of Arizona.

Authors: Tom Hicks and Dianne Patterson

About: This project provides several programs to visualize, compare, and review the image quality metrics (IQMs) produced by the MRIQC program. MRIQC extracts no-reference IQMs from structural (T1w and T2w) and functional (BOLD) MRI data.

Using QMTools via Docker (or Apptainer)

The easiest way to use the QMTools is via the publicly available Docker container or an Apptainer container derived from the Docker image. With this approach, the QMTools, located in the container, are called by auxiliary Bash scripts to process data from input and output directories which the scripts make available to the container. Scripts, examples, and documentation which support and simplify this process are available in the QMTools Support project on GitHub. Since this approach requires only Docker or Apptainer and the bash shell to be installed on your local computer, it has a minimal "footprint".

Note: For documentation on the individual tools and how to use the tools via Docker, please see the QMTools Support project.

Installing with Conda

You can also install the main QMTools project (not the Support project) locally on your computer and run the tools from there. Using Miniconda, you can easily set up an isolated environment to run the QMTools without interfering with other local software.

Installing with a Python Virtual Environment

More knowledgable users can install the main QMTools project (not the Support project) locally using a Python virtual environment.

References

Esteban O, Blair RW, Nielson DM, Varada JC, Marrett S, Thomas AG et al. (2019). Crowdsourced MRI quality metrics and expert quality annotations for training of humans and machines. Sci Data 6: 30.
Esteban O, Birman D, Schaer M, Koyejo OO, Poldrack RA, Gorgolewski KJ (2017). MRIQC: Advancing the automatic prediction of image quality in MRI from unseen sites. PLoS ONE 12: 9.

License

This software is licensed under Apache License Version 2.0.

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qmtools's Issues

qmviolin runs with errors

Running qmviolin produces an HTML report and pngs but also the following error. It does not matter whether there is a specified report directory or not.

Environment:
University of Arizona HPC
Singularity image (pulled from Docker on 2022-03-17 via singularity pull docker://hickst/qmtools)

Call:
singularity exec /groups/adamraikes/singularity_images/qmtools_latest.sif qmviolin T1w fetched/ge_sample.tsv ../mriqc-0.15.1/T1w/group_T1w.tsv -r v0.15.1_violin -v

Error:

(qmviolin): Comparing MRIQC records with modality 'T1w'.
Traceback (most recent call last):
  File "/usr/local/bin/qmviolin", line 8, in <module>
    sys.exit(main())
  File "/usr/local/lib/python3.9/site-packages/qmtools/qmviolin/violin_cli.py", line 119, in main
    violin.make_html_report(modality, args, plot_info)
  File "/usr/local/lib/python3.9/site-packages/qmtools/qmviolin/violin.py", line 121, in make_html_report
    copy_tree(genh.AUX_DIR_PATH, report_dirpath)
  File "/usr/local/lib/python3.9/site-packages/qmtools/file_utils.py", line 15, in copy_tree
    shutil.copytree(from_dir, to_dir, dirs_exist_ok=True)
  File "/usr/local/lib/python3.9/shutil.py", line 563, in copytree
    with os.scandir(src) as itr:
FileNotFoundError: [Errno 2] No such file or directory: 'qmtools/qmviolin/static'

I think it's only affecting some side bar static images, but I'm not sure:

Escape spaces in URL value field

If generating URL for output only need one more escape if any value field contains spaces.

Inconsistency: qmviolin does not run in verbose mode by default

Both qmtraffic and qmfetcher run in verbose mode by default, but qmviolin does not run in verbose mode by default.

Is there any documentation?

Hello! This project sounds very interesting along the lines of mriqc but unfortunately I can't seem to find any documentation or at least some example Jupyter notebooks. Any help? Thanks!

Time out errors with qmfetcher

Running qmfetcher and get timeout errors (irrespective of number of records). Most of the time I can brute force re-run it and get the data but larger and larger samples become increasingly unlikely. I'm trying to get a sufficiently large sample to be able to figure out how the Manufacturer and Model fields are set for GE Discovery MR750s (if at all available). I successfully ran this with -n 300 but that took sever tries with this same error.

Environment:
University of Arizona HPC
Singularity image (pulled from Docker on 2022-03-17 via singularity pull docker://hickst/qmtools)

Call:
singularity exec /groups/adamraikes/singularity_images/qmtools_latest.sif qmfetcher -v T1w -n 500 -o ge_sample.tsv -q ge.qp

Error:

(qmfetcher): Querying MRIQC server with modality 'T1w', for 500 records.
socket.timeout: The read operation timed out

During handling of the above exception, another exception occurred:

urllib3.exceptions.ReadTimeoutError: HTTPSConnectionPool(host='mriqc.nimh.nih.gov', port=443): Read timed out.

During handling of the above exception, another exception occurred:

requests.exceptions.ConnectionError: HTTPSConnectionPool(host='mriqc.nimh.nih.gov', port=443): Read timed out.

Move TrafficLight report to separate Reports subdirectory

Needs its own.