Heudiconv not creating func and dwi folders

Hi all,

I´m a new user of heudiconv since I see how the neuroscience community can benefit from using BIDS.

So far I´ve set up the heuristic.py and it does the conversion correctly. The issue is that all Nifti files end up in the anat folder in the output directory. My question is: Why is heudiconv not creating the func and dwi folders and placing the corresponding Nifti files within?

I´d appreciate any hint to solve this.

Thanks in advance for taking the time to reply.

Best wishes,

Hi Noelia,

It might be helpful if you could post/link to your heuristic.py file, as well as the version of heudiconv you’re using, so we could have a better sense of where things might have gone wrong.


Hi Ursula,

Thanks a lot for offering your help. Here´s a link to my heuristic.py: https://drive.google.com/open?id=1lSJqmJdEET2p23M5bqYxfUDo5aEl8duD

It´s good that you asked about the heudiconv version. I guess I have the latest release (0.5.4) because I installed it with Docker (18.09.7) in Ubuntu by pulling the latest release.

I´m not very familiar with bash or python scripting. I tried using the command heudiconv --version in the bash terminal but it doesn´t recognize it. Should I use a different syntax to check the heudiconv version that I have?



The nifti paths in the heuristic file all point to the ‘anat’ folder. You will need to manually change the paths to point to individual (appropriate) folder. Ie., anat, func, dwi, fmap that comply with the BIDS standard.

BIDS spec:

Heudiconv tutorial:

Hi @gspitz ,

Thank you so much for revising my heuristic.py file. I modified the paths to point to the appropriate folder and that solved the problem.


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