Generic fmri data convertor to BIDS

fmri
neuroimaging
bids

#1

Hello everyone,
:smile:

So I had this database consisting of minc data:

MyDataset/
|
└── adhd_41278_FU12_T1w_001.mnc
|
└── adhd_41278_FU24_T1w_001.mnc
|
└── adhd_41578_BL00_rest_001.mnc
...

That I wanted to convert into BIDS :

MyDataset/
|
└── sub-41278/
|   |
|   └── anat/
|       |
|       └── adhd_41278_FU12_T1w_001.nii
|       |
|       └── adhd_41278_FU24_T1w_001.nii
└── sub-41578/
    |
    └── func/
        |
        └── adhd_41578_BL00_rest_001.nii
...

I googled it and couldn’t find any tools that suit my need. Even using the official .mnc to .nii convertor was not working with the fmri images (mismatch of dimensions in the raw data).

So I came up with this tool that uses nibabel:

It is really hardcoded for now but I plan in to improve the architecture in the future if needed.

So my questions:

  1. Is there any tool somewhere that is already doing that ?
  2. Are they some people interested to contribute to a tool like this ?

Thank you all,


#2

This is very cool! I am not aware of such tool, but the need for it has been obvious for a while.

You should consider sending a Pull Request to https://github.com/bids-standard/bids-website to list your tool among other BIDS tools on https://bids.neuroimaging.io