BIDS import issues

[bkossows]

Hi Alfonso,

I’ve just started working with CONN and I really like it — great work!
While exploring the functionality with BIDS datasets, I noticed a few minor issues and possible improvements that might make the workflow smoother:

1. Copy dataset behavior
   When selecting “Copy dataset” (which I think should be the default), the copied version doesn’t include phase images — only magnitude — which causes an error during preprocessing. It also doesn’t copy the corresponding events.tsv files.

2. Copy speed and alternative suggestion
   Copying datasets currently takes quite a long time. It might be more efficient to offer an alternative option that creates symbolic links to the original files instead of copying them.
   For example:

   cp -rs ~/DATA/sub-01 ./

3. Events TSV import pattern
   When a dataset is manually copied or linked and imported with the default settings, events.tsv files are not imported correctly. It seems the importer looks for filenames like:

   sub-TR19_ses-2_task-move_run-01_bold.nii_events.tsv
   

   To fix this, I suggest removing the .nii part from the filename pattern here, e.g.:

   fname = conn_prepend('', regexprep(tname, '_bold\.nii(\.gz)?$', ''), '_events.tsv');

   This adjustment allows the import to work correctly.

I hope this feedback helps improve the BIDS import process.
Thanks again for your great work on CONN — I really appreciate it!

Best regards,
Bartosz