Hello,
We would like to do field map correction in SPM12 for our EPI data (double echo field map acquisition with a Siemens Skyra), but there is some confusion/debate about some of the methods. I have searched online and on the SPM12 manual but I still cannot find the answers to the following questions:
1) What is the distinction between the "Precalculated Phase and Magnitude Maps" and "Calculate VDM" modules in SPM12? Some people have told me to use one, others to use another.
2) Do you need to bet (skull strip) the magnitude field map? (Do you need to, or should you, skull strip the EPI and anatomical images, if you are using DARTEL segmentation and normalization?)
3) Finally, when I was running a SPM12 script which included the following modules: "Calculate VDM", "Realign and Unwarp", and "Coregister", a Fieldmap Toolbox gui popped up while running the script. This toolbox, similar to what can be seen on
http://www.mccauslandcenter.sc.edu/crnl/tools/fieldmap, included values that did not match the short TE, long TE, and EPI Readout Time that I included in my modified pm_defaults file (which I inputted into the "Calculate VDM" module). Does anyone know what is calling this pop-up, how to prevent it from being called/how to change the values in the pop-up to match the values I included in the pm_defaults file, or a way to confirm that SPM is referencing the values in the pm_defaults file and not in this pop-up?
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