How to convert NIFTI to BIDS along with creating their json sidecars in the process?

[Amrou_Abas]

Hello everyone,

I am fairly new to neuroimaging and I am building an sMRI preprocessing pipeline. I have some confusion regarding the process.

I have a dataset that contains both DICOMs and NIFTIs for each subject. I successfully transformed the DICOMs to NIFTIs and created their JSON sidecar files (using dcm2bids). However, when I tried to use BIDScoin to convert the NIFTIs to BIDS format, it neither renamed the files according to BIDS standards nor generated the necessary JSON sidecar files for them.

What do you advise me to do? Are the JSON sidecars generated from the DICOMs sufficient, or do I need to generate JSON sidecars for the NIFTIs as well? This aspect is a bit confusing to me.

Note: The DICOMs and NIFTIs in the original source data have different tags, so I am unsure if they represent the same data in the end, but I could be mistaken.

Any guidance would be greatly appreciated.

[jsein]

Hi @Amrou_Abas , welcome to NeuroStars! I hope you will like it here!

To start with, these discussions and links to the tools therein may be useful to you:

Convert data to BIDS format

Hi guys, I would like to know if someone has a very generic script I could use to convert my data to BIDS format. My script is not the most efficient and every time I use an other data structure, I have to re-do some modification on the script. It is very time consuming and not very efficient. I would really appreciate, Thanks,

Niifti conversion to BIDS?

A colleague will be sending me a series of nifti files converted with dcm2niix, along with their .json side-cars. These would be single participant, single session. Does there exist a tool that organizes nifti+json pairs into a bids structure, or would this be something I simply need to do manually?

[Amrou_Abas]

Thank you very much for the response! I appreciate it.

[MadhavanSubhashini]

Hi @Amrou_Abas,

Welcome to Neurostars. I’m in the same boat as you. See my question here. Did you figure out how to convert your nii/nii.gz files to BIDS and also create subject specific JSON Sidecars and TSV files.

My post: No DICOMs only Nii files available--creating JSON Sidecars and TSV Files

Thanks.

–Subbi M.

[Amrou_Abas]

Hi @MadhavanSubhashini ,

Actually, I decided on just naming these NIFTIs to be BIDS-conform and that is it. The BIDS validator does not give any error if I did so. Hence, I decided to move on as it is quite complex in my opinion.