[Help] Figuring out how to structure my Nifti Data into the BIDS format

1

Hello there!

These seems like a very simple issue (I feel a little stupid asking about this) but I am very new to the field and have just started working on a project where I need to move Nifti and txt data for 160+ participants into the BIDS format. I have spent the better half of the weekend looking for how this can be done, running through tutorials and a lot of literature, and still seemingly going in circles. With my supervisor ill, I am very lost. Can someone please help me with these:

  • Can this be a folder structure that we can create on our local devices or does it need to be uploaded anywhere? (Like a BIDS repository)
  • Do I need to do this manually or is there a way I can automate the cateogorization of my data into the BIDS format? I have never worked with coding before, so I’m not sure how this would work.
  • How can I validate if my structure is correct?

I know these are very straightforward questions, but being so green in this field has left me no option but to reach out to the community.

Thanks in advance :slight_smile:

2

Hi @siddharthmsc

Can this be a folder structure that we can create on our local devices or does it need to be uploaded anywhere? (Like a BIDS repository)

Turning your NIfTI and txt files into the BIDS format means creating a folder structure and adding metadata files (creating new files that describe aspects of your experiment) --> a BIDS dataset can exist on your local device, it does not have to be uploaded.

Have you checked out the BIDS specification?

Do I need to do this manually or is there a way I can automate the cateogorization of my data into the BIDS format? I have never worked with coding before, so I’m not sure how this would work.

There are a number of tools to help with the conversion. See the list on the BIDS website:

I can’t estimate right now how much coding will be needed (if at all), so I suggest you give it a try.

How can I validate if my structure is correct?

For that, you can use the BIDS validator. Given that you do not have coding experience I suggest that you use the online validator.

Hope this helps!

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Thank you so much for your response @sappelhoff. I have checked the bits specification, and while the folder structure is clear, I’m still figuring out a txt file to Json conversion. Any tips here?

What I meant by automation also was if I could automate the folder heirarchy creation or if I would have to do it manually for all 160+ participants.

Thanks again, your responses were very helpful :slight_smile:

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indeed, this is where a small conversion script would shine. Do you have colleagues or friends that could help you with writing such a script? E.g., in Python?

Else to help you any further, we’d need to know more about the txt files. Perhaps you can upload one of them to a dropbox and share a link?

I am not sure whether one of the tools in the list I linked to may do the job. Else, I’d again suggest a small script.

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Let me check with the lab if I can upload the txt file and share the link :slight_smile: Thanks again for the prompt response!

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Hey @sappelhoff, here is the link to the txt file: https://drive.google.com/open?id=1D6iFRgpnSm0TgBw6yqIkxxCqYRC-Crvf

Another quick question I had - the functional scans have 3 tasks, and each task has been repeated. However, they all form part of the same session. What would be the best way to organize this in the BIDS format. Sorry again if this is a stupid questions - I’m just not being able to get the best information about the same

Thanks

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You can separate tasks within the same session with ses-yoursession_task-yourtask1 ses-yoursession_task-yourtask2 etc… You can also denote different runs or acquisition parameters. This is all explained in the BIDS specifications that others have linked.