fMRIPrep skips fieldmap correction!

[majidsaberi]

Hello everyone,

I have fieldmap images in BIDS format in my data but fMRIPrep skips fieldmap correction step. I wonder what’s happening in the analysis. Do I conclude that my images are not distorted, then it’s skipped automatically by fMRIprep or there is an error?

[Steven]

Hi @majidsaberi ,

Do you have the IntendedFor or B0FieldSource/B0FieldIdentifier fields filled out in your fmap jsons?

Best,
Steven

[majidsaberi]

Hi Steven and thanks for your helps!

No, I do not have, should I include them?
The scanner is Siemens, is there any specific format for that?

Thanks

[Steven]

Yes, you need either of those, and nothing specific needed for Siemens data.

An example IntendedFor in your fmap jsons would be

“IntendedFor”: [“func/sub-01_task-rest_run-01_bold.nii.gz”,
“func/sub-01_task-rest_run-02_bold.nii.gz”]

Of course, replace with the paths and names for your data.

Best,
Steven

[tiborauer]

Utilize TOPUP fieldmap data into fMRIprep

As far as I can see, fMRIPrep uses no susceptibility-derived distortion correction (phase-difference or pepolar) at all! That is what I found on the fMRIPrep’s readthedocs: “Please note that all routines for susceptibility-derived distortion correction have been excised off of fMRIPrep”

[Steven]

@Utilize TOPUP fieldmap data into fMRIprep

Please note that all routines for susceptibility-derived distortion correction have been excised off of fMRIPrep

Hi @tiborauer,

This is just saying that the development of SDC routines is no longer in the fMRIPrep repo. fMRIPrep still very much does SDC, but does so by invoking another software SDCFlows. This is similar to the anatomical workflow, which is done by calling another external software, sMRIPrep.

Best,
Steven

[tiborauer]

(edited because continued on different post instead)