search

aramis-lab / clinica

Software platform for clinical neuroimaging studies
http://www.clinica.run/
Other
218 stars 72 forks source link

Some clinical CSV files downloaded by users contain double quotes #1136

Open tharpm95 opened 2 months ago

tharpm95 commented 2 months ago

Describe the bug When downloading the necessary CSV files from the ADNI data portal, the format of the downloaded CSV does not appear to match what is expected with the code. It contains double quotes across all cells e.g. ""Column 1"" ""Column 2"" ""Column 3"" leading to an issue during parsing the contents of the CSV file.

To Reproduce Steps to reproduce the behavior:

  1. Download the latest versions of CSVs
  2. Run ADNI-to-BIDS conversion

Expected behavior From what I can gather, for some users, no error may occur at all. For others, the error may occur pertaining to double quotes.

Suggested resolution Provide exceptions to handle cases where the CSV contains double quotes.

tharpm95 commented 2 months ago

Closing the issue upon noticing recent changes with the load_clinical_csv function

tharpm95 commented 2 months ago

Upon closer inspection load_clinical_csv does not solve the issue, but quote handling can likely be integrated into that function