fMRIprep with NIFTI and metadata text file (no DICOMs)

1

Hello All,

Is it possible to convert metadata text file (with its nifti file) to the appropriate json file so it is compatible with the BIDS format?

Thank you very much in advance
J

2

Hi,

What metadata text file are you referring to? If you have your original dicoms, you can use dcm2niix/dcm2bids to get your BIDS-compliant json files.

Best,
Steven

3

Hey Steven,
Thanks for getting back to me.
Unfortunately, I don’t have the dicoms but only the fmri nifti file with a text file containing some of the info about the dataset (for example it misses the slice timing information).
Is there any way I can create the .json file from the text file?

Thanks in advance

4

Unfortunately information in the JSON are designed to be everything that you can’t get from a Nifti header, so unless you have either your dicoms or scanner protocols, I don’t see how you’d be able to recover that kind of information.

5

Thanks again.
That is what I thought.
I will try and obtain the scanning protocol, do you know what type of scanner protocol would I need in order to create the JSON? And what toolbox/function could I use?

Many Thanks
J

6

I can’t think of any toolbox unfortunately. The default protocol that is produced by the scanner should suffice.

7

Cool. And then just creating the JSON file manually?

8

Yes, although there may be some individual metadata points (like each subject’s slice timing) that I don’t see how one would be able to recover.

9

Exactly my thinking. In theory, I could disable slice timing with the command “–ignore slicetiming”. What do you think?

10

That should work fine.