DICOM to BIDS conversion on Windows

Dear all,

I have always converted my data on Linux or Mac using dcm2bids:

but it does not work on Windows (for me). The only way I have found is using dcm2nii tool of MRIcron.

Is there any tool working nice on Windows, without doing much stuff manually (like creating folders, renaming files etc.)?

Any help would be appreciated!

Best,

Dima

Hi @Dmitriy_Desser

Thank you for your question! Perhaps using the python based HeuDiConv will work (since you have access to the dicom files). This utilizes dcm2niix which has windows capability. We have a tutorial that walks through how to use it. The tutorial was written using a MacOS, but the process should be the same.

Thank you,
Franklin

If HeuDiConv does not natively work on Windows, you should still be able to use the Docker image.

@franklin
@effigies

Hi,

Thank you guys for your replies!

Yes, this is exactly the problem… We still have Windows 7 in our lab, so it is not possible to run docker. Is there any possibility to run heudiconv without docker?

So the only way would be to write a python or matlab script for the conversion for each study separately or to do everything manually with MRICron, right?

Best,

Dima

HeuDiConv is written in Python. If you install all of its dependencies, then you should be able to run it natively on Windows.

@effigies
@franklin

Thank you guys! It almoust wotks!

The only error I am currently not know how to deal with is:

What do you actually think about developing some kind of compiled version with GUI for heudiconv using QT?

I mean I could try it on my own (I am currently MD student) but any supervision/support would be very nice…

Best,

Dima

Hi @Dmitriy_Desser

Thank you for your message and traceback! It appears to be using a prescribed exisiting file (perhaps from a previous attempt). May you try to delete the hidden heudiconv folder and try again? I noticed if I still had the folder and ran again some errors that were fixed were reverted. Unfortunately I am not sure what the error message is saying exactly either :slight_smile: .

I think developing a compiled GUI version would be helpful! May be raising this in their issues will bring more attention and there may be others that are thinking of the same thing! (this thread may not have been noticed by the developers)

Thank you,
Franklin

@Dmitriy_Desser, dcm2bids should work on Windows, it’s just not well tested there. Are you hitting the same error I hit, https://github.com/cbedetti/Dcm2Bids/issues/79 ?

If so, you can try installing my patch by running:

pip uninstall dcm2bids # get rid of the official version
pip install dcm2bids@git+git://github.com/kousu/Dcm2Bids@package-find_packages

Normally I don’t recommend installing random software from strangers off the internet to people like this, so please take some time to look through the code in my patch to verify I’m not trying to hack you!