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).
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.
Several issues in this section that make it hardly understandable:
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).
https://github.com/aramis-lab/clinicadl_handbook/blob/a1a56b20938bc683b6d1fa4d43e6ae9330e15730/src/label_extraction.py#L133-L135
If
oasis_after_qc.tsv
andadni_after_qc.tsv
are outputs ofquality-check
procedure, they should be nameddata_oasis/QC_result_t1.tsv
anddata_adni/QC_result_pet.tsv
, to be consistent with: https://github.com/aramis-lab/clinicadl_handbook/blob/a1a56b20938bc683b6d1fa4d43e6ae9330e15730/src/preprocessing.py#L423-L428https://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
andcheck-missing-modalities
procedures, but not the output ofquality-check
procedure. So, the procedureget-labels
cannot be run properly with the--restriction_tsv
option. Maybe it is whatoasis_after_qc.tsv
andadni_after_qc.tsv
refer to, but I can't find them on the AramisLab server.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.