Distortion correction with epi spin echo and not gradient

Software Support
,
1

Summary of what happened:

I am running fmriprep on two different subjects; one with ap/pa spin echo, and one with pa only gradient echo.

For the gradient echo, it works well (and only with one PA because my sequence is in ap), fmriprep does the distortion correction. In the fmap folder I see :

- sub-05_ses-1_task-priming_run-1_dir-pa_epi.nii.gz
- sub-05_ses-1_task-priming_run-1_dir-pa_epi.json

And in the json file it is intended for the task:
- "IntendedFor": ["bids::sub-05/ses-1/func/sub-05_ses-1_task-priming_run-1_bold.nii.gz"]

However, for the spin echo, fmriprep does not do distrortion corrections, and in a the fmap folder I see:

- sub-06_task-priming_run-1_dir-ap_epi.bval
- sub-06_task-priming_run-1_dir-ap_epi.bvec
- sub-06_task-priming_run-1_dir-ap_epi.json
- sub-06_task-priming_run-1_dir-ap_epi.nii.gz

and same for pa:

- sub-06_task-priming_run-1_dir-pa_epi.bval
- sub-06_task-priming_run-1_dir-pa_epi.bvec
- sub-06_task-priming_run-1_dir-pa_epi.json
- sub-06_task-priming_run-1_dir-pa_epi.nii.gz

Both intended for : “IntendedFor”: [“bids::sub-06/func/sub-06_task-priming_run-1_bold.nii.gz”]

Do you have any idea what is happening?

Thank you !!

Version:

24.1.0

Environment (Docker, Singularity / Apptainer, custom installation):

Ubuntu

Data formatted according to a validatable standard? Please provide the output of the validator:

PASTE VALIDATOR OUTPUT HERE

Relevant log outputs (up to 20 lines):

PASTE LOG OUTPUT HERE

Screenshots / relevant information:

2

There’s a bug in collecting gradient-echo fieldmaps with bids:: in their IntendedFor fields. Just remove bids::sub-<label>/ and it should work.

3

Thank you for you answer!

You meant for spin echo? Because for gradient it works perfectly with bids::sub-/

Best,

4

I thought it was the other way around, but either way, the subject-relative URIs are well-supported, and there will be a fix for BIDS-URIs in the next release.

5

Hi @Alexane_Leclerc,

I think you are going to run in BIDS validation errors trying to put a task-<> label in your fmap file names. You should make sure your files are BIDS compliant before rerunning fmriprep.

Best,
Steven

6

Ok I will try without then and see!

7

Hi!
Oh, but can I still write run-1?
Because otherwise how do you differentiate?
I have only shown one run for the task, but I also have fmap for 3 other tasks, and the files can’t have the same names!
For instance, here is how my fmap folder is organised, and for this (so only PA gradient echo), everything worked perfectly!

Capture d’écran du 2024-10-25 17-16-57
Capture d’écran du 2024-10-25 17-16-57950×660 149 KB

Best,

8

Hi @Alexane_Leclerc

See naming conventions here: Magnetic Resonance Imaging - Brain Imaging Data Structure 1.10.0

Yes.

You can use the acq-<> label too, which is a pretty flexible entity. E.g., acq-movie to indicate a fmap is going to the movie task.

Best,
Steven

9

Oh there is is yes! Perfect thank you!!