Dear Juan,
>
> I appreciate the previous message in this thread was posted quite a while, but regarding method 2 (using topup to generate the field map in Hz from opposite blip), which can then be used in SPM to generate the VDM, as per the instructions at LCNI (https://lcni.uoregon.edu/kb-articles/kb-0003), there are a couple of parameters that need to be indicated when choosing this option but LCNI do not provide details in this regard.
>
> When selecting the option "Precalculated FieldMap (in Hz)" in the "Calculate VDM" batch module, you still have to specify the FieldMap defaults. Here you can choose Defaults values or Defaults file. With default values, you are asked to provide the field map's short and long TE. However, as you are using the reverse blip method, there are no short and long TEs to include here. And choosing the defaults file is no use as this file just provides short and long TEs for an Allegra scanner. Anyway, not sure if the echo time difference used by FieldMap and FUGUE makes sense in the context of a reversed blip method for distortion correction. But if there are values here that can justifiably be entered for short and long TE, I'd greatly appreciate someone providing them.
this is really more of a question for the SPM mailbase, so you might get a more certain answer there.
My 5c is that I doubt that the TE values are used at all when you use the "Precalculated FieldMap” option. There is no reason to. It is probably just a matter of a slightly clunky GUI. The thing you would want to get right is the “TOTAL_EPI_READOUT_TIME”, which I think should be the same value as the fourth column in your topup acqparams file, but multiplied by a 1000.
Jesper
>
> Regards,
>
> Juan
>
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