adni-to-bids converter

[Remi Silva]

Hi 

I am not sure what I am doing wrong.

I have downloaded all original, preprocessed, and postprocessed images for my subjects, and have downloaded all tabular data (CSV) from ADNI and saved them under CLINICAL_DATA_DIRECTORY but I keep getting this error message, I have checked the contents and the clinical CSV files are there:

lib/python3.10/site-packages/clinica/iotools/converters/adni_to_bids/adni_utils.py", line 981, in create_adni_sessions_dict
    raise ValueError("Empty dataset detected. Clinical data cannot be extracted.")
ValueError: Empty dataset detected. Clinical data cannot be extracted.

[Remi Silva]

I have re-installed clinica and the newest release is running (clinica 0.8.1). I have rerun the converter without the subject list to see if this was the issue but I got this error log:

Expecting to find exactly one file in folder my_clinical_data_path pattern DXSUM_PDXCONICAL_DATA_DIRECTORY matchingV_ADNIALL(_\d{1,2}[A-Za-z]{3}\d{4})?.csv. 0 files were found instead :
[- ]

[Nicolas Gensollen]

Hi,

What does your folder "my_clinical_data_path" look like ?

The CSV file DXSUM_PDXCONV_ADNIALL has been renamed a few months ago to DXSUM_PDXCONV and we adapted the converter in the patch release 0.8.1 to work with both (basically, it tries to read the old file and if it cannot find it, it tries to read the new one).

To give you an example, I downloaded the clinical data on April 29th, and the csv file I have is named DXSUM_PDXCONV_29Apr2024.csv.

Best,

Nicolas

[Remi Silva]

Hi Nicolas,

The path file is correct i double checked with the terminal to get the realpath,  the clinical data directory has 305 csv files and there is a file named: DXSUM_PDXCONV_26Jun2024.csv
thank you

Renata

[Nicolas Gensollen]

Hmm, looks like everything is fine. I don't see why you get this FileNotFoundError... 🤔

Could you paste the error trace you get ?

Best,

Nicolas