hickst / qmtools Goto Github PK

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:

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!

Needs its own.

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.

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

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