Qsiprep and flair images

Software Support
1

Dear Neurostars community,

We have a (bids formatted) dataset containing T1w, FLAIR, diffusion and a b=0 image with reversed phase encoding direction for distortion correction. We launched preprocessing with qsiprep with success, however there does not seem to be any FLAIR in the output. The original data is organized as follows:

.
├── dataset_description.json
├── README
└── sub-0105
    ├── anat
    │   ├── sub-0105_FLAIR.json
    │   ├── sub-0105_FLAIR.nii.gz
    │   ├── sub-0105_T1w.json
    │   └── sub-0105_T1w.nii.gz
    ├── dwi
    │   ├── sub-0105_dwi.bval
    │   ├── sub-0105_dwi.bvec
    │   ├── sub-0105_dwi.json
    │   └── sub-0105_dwi.nii.gz
    └── fmap
        ├── sub-0105_dir-LR_epi.json
        └── sub-0105_dir-LR_epi.nii.gz

Is there a way to ask for FLAIR co-registration in qsiprep?

Thanks for your help!
Manu.

2

Hi @ecaruyer, and welcome to neurostars.

At this point qsiprep can only use t1w or t2w anatomical images.

Best,
Steven

3

Hi @Steven, Thanks for your swift reply, this is very helpful!

Best,
Manu.