Getting ihmt data into BIDS format

1

Hi everyone,

I am new to BIDS (developing it on shell) and I actually have a simple question. Is it possible to create a folder other than anat or func for example like ihmt and keep the same structure (sub-01_ses-01_mt or m0) and actually be compatible with BIDS format?
My goal is to make BIDS data and be able to visualize them using the filetree of fsleyes.

Thank you!
Amira

2

Hi @Amira

Thank you for your question! Yes this is possible. This can be another folder (as you mentioned) at the same level as anat and func. This folder will be added to the .bidsignore file because the bids validator will flag this as an error (because it is not specified yet). It will be interesting to see if this will keep the folder visible to fsleyes!

Thank you,
Franklin

3

Thank you!
I will try this and get back to you.

4

Hello again,

So this morning I tried adding the .bidsignore file to my directory at sub-* files level but it doesn’t seem to work.
Also I’ve noticed an error when I try to open my .json file in fsleyes filetree.

json_file_problem
json_file_problem1665×608 108 KB

What am I missing?

Thank you for your help!
Amira

5

Hi @Amira

May you please clarify when you say it does not work? It does not work to appear in the fsleyes filetree? This appears you are trying to overlay a json on a nifti image? These are incongruent file types for visualization. The json file is providing metadata regarding your data. In the case of the dataset_description it is about the dataset.

Thank you,
Franklin

6

Hi,
Thank you for your answer and sorry if I was not clear.
I will try to explain better. First, the .bidsignore file did not work and I kept getting errors but I found my mistake and now my data are perfectly organized in a BIDS way. Then, I tried visualizing them with the filetree, the anatomic file was visible even with the T2stir (which I added to the .bidsignore file) but not my ihmt file which is supposed to be at the same level as the anat_image file.

Thank you,
Amira

7

Hi @Amira

Great to hear the dataset passes the BIDS Validator! Perhaps this folder (ihmt) is not supported for visualization through FSLeyes yet? There may be some options in the software to enable this. Perhaps raising it with the FSLeyes and hear their advisement? This feature is relatively new.

Thank you,
Franklin

8

Hi,
Thank you!
I will be looking into Fsleyes software and see what I can do.

Thank you again for your help.
Amira