aramis-lab / clinicadl_handbook

Tutorial to use (new version of) clinicadl (>1.0.3)
https://aramislab.paris.inria.fr/clinicadl/tuto/2023/html/
Creative Commons Zero v1.0 Universal
0 stars 6 forks source link

Clarification needed in tsvtools section #27

Closed thibaultdvx closed 7 months ago

thibaultdvx commented 7 months ago

Several issues in this section that make it hardly understandable:

  1. https://github.com/aramis-lab/clinicadl_handbook/blob/a1a56b20938bc683b6d1fa4d43e6ae9330e15730/src/label_extraction.py#L122-L129

    these lines don't show (supposedly fixed in #20, but not yet visible). Besides, it could be mentioned that it is OASIS1 that should be downloaded (and up to participant 107). And finally, I'm not even sure that it useful to ask the user to download the data, since they are not used in the section (unless the user wants to run the whole preprocessing pipeline on the whole dataset, which seems to be out of the scope of this handbook).

  2. https://github.com/aramis-lab/clinicadl_handbook/blob/a1a56b20938bc683b6d1fa4d43e6ae9330e15730/src/label_extraction.py#L133-L135

    If oasis_after_qc.tsv and adni_after_qc.tsv are outputs of quality-check procedure, they should be named data_oasis/QC_result_t1.tsv and data_adni/QC_result_pet.tsv, to be consistent with: https://github.com/aramis-lab/clinicadl_handbook/blob/a1a56b20938bc683b6d1fa4d43e6ae9330e15730/src/preprocessing.py#L423-L428

  3. https://github.com/aramis-lab/clinicadl_handbook/blob/a1a56b20938bc683b6d1fa4d43e6ae9330e15730/src/label_extraction.py#L137-L139

    The user has the possibility to download the outputs of merge-tsv and check-missing-modalities procedures, but not the output of quality-check procedure. So, the procedure get-labels cannot be run properly with the --restriction_tsv option. Maybe it is what oasis_after_qc.tsv and adni_after_qc.tsv refer to, but I can't find them on the AramisLab server.

  4. https://github.com/aramis-lab/clinicadl_handbook/blob/a1a56b20938bc683b6d1fa4d43e6ae9330e15730/src/label_extraction.py#L180 This command raises Error: Missing argument 'OUTPUT_DIRECTORY' because no directory for the output .tsv file is given.

thibaultdvx commented 7 months ago

Regarding 2., it is explained at the end of the section:

https://github.com/aramis-lab/clinicadl_handbook/blob/a1a56b20938bc683b6d1fa4d43e6ae9330e15730/src/label_extraction.py#L196-L202

thibaultdvx commented 7 months ago

Regarding 3., oasis_after_qc.tsv and adni_after_qc.tsv are on github.