Dear Katie,
On 25/01/17 19:38, Katie Jankowski wrote:
> 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.
This should be the same. Older versions of SPM had four separate modules
for FieldMap (presubstracted, re/im, phases, precomputed) with a lot of
duplicated code but this has been changed such that there is now a
single "Calculate VBM" with four options inside (entry "field map").
> 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?)
I don't think so as the FieldMap toolbox will itself perform
segmentation to calculate a brain mask.
> 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?
This interface shouldn't appear and should actually be entirely removed
from the SPM source code. I'll look into this.
Best regards,
Guillaume.
--
Guillaume Flandin, PhD
Wellcome Trust Centre for Neuroimaging
University College London
12 Queen Square
London WC1N 3BG
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