adni-to-bids ValueError: Empty dataset detected. Clinical data cannot be extracted.

[Scott Gurney]

Hi

New user, hoping to use Clinica for my 3rd Year uni project, but I am struggling to convert my ADNI data to BIDS format.

I am using Clinica 0.7.6 and Python 3.8

Traceback (most recent call last):
  File "/gpfs/home/tqh20wsu/.conda/envs/clinicaEnv/bin/clinica", line 8, in <module>
    sys.exit(main())
  File "/gpfs/home/tqh20wsu/.conda/envs/clinicaEnv/lib/python3.8/site-packages/clinica/cmdline.py", line 92, in main
    cli()
  File "/gpfs/home/tqh20wsu/.conda/envs/clinicaEnv/lib/python3.8/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
  File "/gpfs/home/tqh20wsu/.conda/envs/clinicaEnv/lib/python3.8/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
  File "/gpfs/home/tqh20wsu/.conda/envs/clinicaEnv/lib/python3.8/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/gpfs/home/tqh20wsu/.conda/envs/clinicaEnv/lib/python3.8/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/gpfs/home/tqh20wsu/.conda/envs/clinicaEnv/lib/python3.8/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/gpfs/home/tqh20wsu/.conda/envs/clinicaEnv/lib/python3.8/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
  File "/gpfs/home/tqh20wsu/.conda/envs/clinicaEnv/lib/python3.8/site-packages/clinica/iotools/converters/adni_to_bids/adni_to_bids_cli.py", line 74, in cli
    adni_to_bids.convert_clinical_data(
  File "/gpfs/home/tqh20wsu/.conda/envs/clinicaEnv/lib/python3.8/site-packages/clinica/iotools/converters/adni_to_bids/adni_to_bids.py", line 147, in convert_clinical_data
    adni_utils.create_adni_sessions_dict(
  File "/gpfs/home/tqh20wsu/.conda/envs/clinicaEnv/lib/python3.8/site-packages/clinica/iotools/converters/adni_to_bids/adni_utils.py", line 980, in create_adni_sessions_dict
    raise ValueError("Empty dataset detected. Clinical data cannot be extracted.")
ValueError: Empty dataset detected. Clinical data cannot be extracted.
(clinicaEnv) [tqh20wsu@c0006 ~/Documents/test]$ ValueError: Empty dataset detected. Clinical data cannot be extracted.

[Matthieu Joulot]

Hi Scott,

Can you tell me what data you are using from ADNI ? As in ADNI-1/ADNI-2/ADNI-3..

Also, have you followed the instruction we suggest in the documentation ? We do not convert every single format from ADNI, you might very well have downloaded only images we do not account for.

If not, could you please try to download your collection like we suggest it here ?

Have a good day,

Matthieu

[Scott Gurney]

Hi  Matthieu

I did follow the instructions, with the exception of the below stage as I could not find those options on the page

I searched for:

SUBJECT -> Subject ID: 007_S_6341

STUDY/VISIT: [ADNI Screening, ADNI3 Year 1 Visit, ADNI3 Year 2 Visit, ADNI3 Year 3 Visit, ADNI3 Year 4 Visit, ADNI3 Year 5 Visit, ADNI3 Year 6 Visit] OR

IMAGE -> Modality: DTI AND fMRI

This should give the following imageIDs:

990573, 990583, 1178798, 1178811, 1329727, 1329738, 1461578, 1461594 

Thank you, Scott

[Matthieu Joulot]

Alright ! This website can be tough to navigate. These options are located under the advanced search button in the "search options" section, as you can see on this screenshot:

Can you download the images from your collection with these boxes ticked ? You should get some images converted afterwards

Have a good day,

Matthieu

[Scott Gurney]

I have downloaded the data again, now seeing those settings (they were already all ticked), using the previous filters, see below.

However when I ran again, I got the same error message:

I will download some different subjects and test again

[Scott Gurney]

I think it may have worked with the other subjects.

Would my first attempt have failed due to it being *_MB_* in the folder names?
i.e. Axial_MB_DTI rather than Axial_DTI

[Matthieu Joulot]

Yes. We do not convert these series, as you can see in this screenshot from the documentation