What would you like to see added in fMRIPrep?
After upgrading fMRIPrep from 24.1.1 to 25.2.3, we noticed a change in fieldmap selection for susceptibility distortion correction (SDC). Previously, fMRIPrep would raise an error when multiple fieldmaps matched a BOLD run (via IntendedFor). The current version proceeds without warning, apparently selecting only the first available fieldmap.
This is problematic because repeated fieldmap acquisitions are often intentional. In our tests, we compared SDC results obtained using different fieldmaps (same position, after repositioning/re-shimming, and from another session) and evaluated the resulting preprocessed BOLD images using registration cost functions. Not always the fieldmap that nominally matches a BOLD run provides the best correction, particularly if there were some artifacts. In the end, the most robust approach was simply to use all available fieldmaps.
Would it be possible to support using all matching fieldmaps for SDC estimation instead of automatically selecting the first one? This appears straightforward to implement with TOPUP, and we are currently using a custom preprocessing step that combines multiple fieldmaps into a single pre-cooked fieldmap.nii.gz/magnitude.nii.gz pair before running fMRIPrep.
Kind regards,
Bartosz Kossowski
Nencki Institute
Do you have any interest in helping implement the feature?
Yes
Additional information / screenshots
No response
What would you like to see added in fMRIPrep?
After upgrading fMRIPrep from 24.1.1 to 25.2.3, we noticed a change in fieldmap selection for susceptibility distortion correction (SDC). Previously, fMRIPrep would raise an error when multiple fieldmaps matched a BOLD run (via IntendedFor). The current version proceeds without warning, apparently selecting only the first available fieldmap.
This is problematic because repeated fieldmap acquisitions are often intentional. In our tests, we compared SDC results obtained using different fieldmaps (same position, after repositioning/re-shimming, and from another session) and evaluated the resulting preprocessed BOLD images using registration cost functions. Not always the fieldmap that nominally matches a BOLD run provides the best correction, particularly if there were some artifacts. In the end, the most robust approach was simply to use all available fieldmaps.
Would it be possible to support using all matching fieldmaps for SDC estimation instead of automatically selecting the first one? This appears straightforward to implement with TOPUP, and we are currently using a custom preprocessing step that combines multiple fieldmaps into a single pre-cooked fieldmap.nii.gz/magnitude.nii.gz pair before running fMRIPrep.
Kind regards,
Bartosz Kossowski
Nencki Institute
Do you have any interest in helping implement the feature?
Yes
Additional information / screenshots
No response