Dear all,
I would like to consult with you regrading using FSL TOPUP and SPM Fieldmap Toolbox for EPI correction.
In our scanning protocol, we acquire multiband EPI sequence for the functional scans and two series of Spin-Echo images (A-P and P-A) for field map correction. Therefore, as suggested, I will use TOPUP to calculate the field map image and then use the SPM Fieldmap toolbox to generate Voxel Displacement Map (VDM) for EPI correction. Here are my two technical questions:
1. I understand that in TOPUP, I need to use the FSL definition of "Total EPI Readout Time" to calculate the field map. However, after this step, when I need to apply the field map in the SPM Fieldmap toolbox, what type of "Total EPI Readout Time" should I input in SPM? (the SPM or the FSL definition?)
2. In the current approach, is it correct that I don't need to worry anything about the short and long TE section in SPM?
Thank you very much in advance for any advice.
Best
Vince
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