Best practices in fieldmap distortion estimation - fmriprep

[Mark_Orloff]

Hi all,

I am new to using fmriprep and trying to determine best practices for distortion correction. My scanning protocol includes both the blip-up/blip-down scans and a GRE sequence. I saw in the fmriprep documentation that the blip-up/blip-down scans take priority for distortion correction (if both types of scans are available and ‘intended for’ the task runs), but I was wondering if anyone knew how this decision was made (i.e., any studies?) or if they have any personal experience with which type of distortion correction tends to work better.

Thanks!
Mark Orloff

[Mark_Orloff]

I was having difficulty finding the relevant fmriprep documentation but here it is quoted below from the 0.8.0 version. I specified in all the fmap scans I had (from both the blip-up/blip-down and GRE sequences) that they were IntentedFor the task runs, and this documentation still appears to be accurate (i.e., fmriprep automatically selected blip-up/blip-down instead of GRE/phase difference B0 estimation)

Fieldmap estimation and unwarping workflows

Automatic selection of the appropriate SDC method

If the dataset metadata indicate tha more than one field map acquisition is IntendedFor (see BIDS Specification section 8.9) the following priority will be used:

1. Phase Encoding POLARity (PEPOLAR) techniques (or blip-up/blip-down)
2. Direct B0 mapping sequences
3. Phase-difference B0 estimation
4. Fieldmap-less estimation (experimental)

[jsein]

There is still a debate in the community to decide which method is the best for SDC.

Here are some articles (it is a non exhaustive list) comparing the different methods:

• Abreu, R.; Duarte, J. V. Quantitative Assessment of the Impact of Geometric Distortions and Their Correction on FMRI Data Analyses. Front. Neurosci. 2021, 15, 642808. Frontiers | Quantitative Assessment of the Impact of Geometric Distortions and Their Correction on fMRI Data Analyses.

• Schallmo, M.; Weldon, K. B.; Burton, P. C.; Sponheim, S. R.; Olman, C. A. Assessing Methods for Geometric Distortion Compensation in 7 T Gradient Echo Functional MRI Data. Hum Brain Mapp 2021, 42 (13), 4205–4223. https://doi.org/10.1002/hbm.25540.

• Clarke, W. T.; Mougin, O.; Driver, I. D.; Rua, C.; Morgan, A. T.; Asghar, M.; Clare, S.; Francis, S.; Wise, R. G.; Rodgers, C. T.; Carpenter, A.; Muir, K.; Bowtell, R. Multi-Site Harmonization of 7 Tesla MRI Neuroimaging Protocols. NeuroImage 2019, 116335. Redirecting.

• Gu, X.; Eklund, A. Evaluation of Six Phase Encoding Based Susceptibility Distortion Correction Methods for Diffusion MRI. Front. Neuroinform. 2019, 13, 76. Frontiers | Evaluation of Six Phase Encoding Based Susceptibility Distortion Correction Methods for Diffusion MRI.

With different conclusions in each. One thing is almost certain now, it is better
to do SDC than to not do it:

Togo, H.; Rokicki, J.; Yoshinaga, K.; Hisatsune, T.; Matsuda, H.; Haga, N.; Hanakawa, T. Effects of Field-Map Distortion Correction on Resting State Functional Connectivity MRI. Front. Neurosci. 2017, 11, 656. Frontiers | Effects of Field-Map Distortion Correction on Resting State Functional Connectivity MRI.

Please note that all routines for susceptibility-derived distortion correction have been excised off of fMRIPrep for utilization on other projects (e.g., dMRIPrep). For more detailed documentation onSDC routines, check on the SDCFlows component.

This means that for FMRIPREP v21.0.0 and later, you have to look at how SDCFlows is dealing with priority for distorsion correction. It is not documented but I found the answer in this thread:

Fieldmaps for multiple techniques