Is it possible to convert nifti files into BIDs format?

[kkdu...@gmail.com]

Dear BIDs experts,

I am working on MRIQC analysis, which requires the BIDs format as input. I have checked the converting tools available on BIDs website, the DICOM to BIDs tool is available. But I have on DICOM files and only have nifti files available, I am wondering is there any functions that I can use to convert nifti files into BIDs format?

Thanks,

Kathy

[Chris Gorgolewski]

Hi Kathy,

Just to clarify BIDS is a bit different than a file format - it is a way of organizing and annotating a set of files. It uses nifti so you don't need to convert any files. One thing that you will most likely to do is creating additional files with metadata. Those will be in JSOn format. Taking your niftis and creating a BIDS compatible dataset should not be too hard though.

Some resources to get you started:

- paper that includes a conversion guide: https://www.nature.com/articles/sdata201644

- specification: http://bids.neuroimaging.io/bids_spec1.0.2.pdf

- validator: https://github.com/INCF/bids-validator (great for checking if the outputs of your work are indeed BIDS compatible)

- example datasets https://github.com/INCF/BIDS-examples

I hope this helps!

Best,

Chris

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[dhruv....@kitware.com]

Hi Kathy,

Any luck in structuring your data in BIDS format? I am also working on MRIQC right now and need some help to format my data in accordance to the BIDS format.

Thanks,

Dhruv

[Franklin Feingold]

HI Dhruv, 

Thank you for your question. There are a number of tools that can accomplish this (from nifti) https://bids.neuroimaging.io/ (they are located under benefits -> converters, although some may not be nifti, but from dicom). One tool from nifti is HeuDiConv (https://github.com/nipy/heudiconv) and there is a tutorial (http://reproducibility.stanford.edu/bids-tutorial-series-part-2a/) that walks through how to use it. 

Thank you,

Franklin

[dhruv....@kitware.com]

Hi Franklin,

Thanks for sharing those links. I had gone through HeuDiConv and that tutorial earlier as well, but they seem to be made for dicom images only as it uses dcm2niix under the hood. I had found this tool bidsify(https://github.com/NILAB-UvA/bidsify) but was struggling with making its config file. Thanks again for your reply.

Regards,

Dhruv

[Raymond Bonnefoie]

Hi Dhruv, 

Thanks for your message, but could you specify if you have succeeded with bidsify ?

thanks

[dhruv....@kitware.com]

Hi Raymond,

I haven't been able to get my config.yml file correct. Still trying it.

[Raymond Bonnefoie]

I had also some difficulties running BIDSify ; so I gave up ….(my input were DICOM files so I used heudiconv)

From nifti, there is also an alternative that i didn't try :BIDSCoin (I saw it in the OHBM program) https://github.com/Donders-Institute/bidscoin

Good luck

[dhruv....@kitware.com]

Raymond,

Thanks for the link. Can you please also share some good resource for heudiconv as I am thinking to convert nifti to dicom and then use it?

Regards

Dhruv

[Raymond Bonnefoie]

Here is a usefull link for heudiconv : 

http://reproducibility.stanford.edu/bids-tutorial-series-part-2a/

Regards