kdestasio / bidsqc Goto Github PK

If bidsQC.py is run on the same subjects multiple times, the run-## string is duplicated each time.

To facilitate quality control, it'd be great to print the series number along and the renamed run number to the output log for the bidsQC.py script.

New link should be https://unfmontreal.github.io/Dcm2Bids/tutorial/.

would it be possible to add info in the bids conversion output files to reflect the series name of the files being copied over? for example, if there are 3 functional runs, and only two make it into pretty bids format, the output might say "error: wrong number of files; largest file copied", but it would be nice to know the original name of the file too.

Currently, the qualitycheck.py script will move files that do not match the template established in the file qualitycheck_config.py to the temporary directory specified in the configuration file. Moving files should be made an explicit option in the config file just as renaming files is an explicit option.

The default behavior of the qualitycheck.py script should be set to produce a log that describes the dataset, but does nothing to the files themselves. Explicit options can then be set to move or rename files based on whether they adhere to the config file specifications.

May be a project specific issue. Will examine further.

The current output of the qualitycheck.py script is lengthy and difficult to use. It is split into output and error logs, but the content of each is not intuitive. Refine the output so it is more user friendly.

The dcm2bids_batch.py script currently requires a session number in the third column of the subject_list.txt file. That number is used to create the ses-label portion of file names when converted into BIDS. However, the BIDS spec does not expect a ses- tag in the file name for data collected within a single session. It would make sense to have an option that can select for single session data or multiple session data and that names the files accordingly with or without the ses- tag.

Here is the error if a user tries to omit session information from the subject_list.txt file

Traceback (most recent call last):
  File "dcm2bids_batch.py", line 105, in <module>
    main()
  File "dcm2bids_batch.py", line 17, in main
    batch_jobs(cfg.subjectlist, cfg.path_dicoms, cfg.path_config, cfg.path_bidsdata)
  File "dcm2bids_batch.py", line 27, in batch_jobs
    wave = entry.split(",")[2]
IndexError: list index out of range

To avoid the script breaking on any one subject, it'd be great if the script ran in parallel via batch submission.