Hi Andrew,
There are many ways to run fugue, but if you load in a fieldmap in rad/s then you just
need the dwell time of the EPI, and do not need the dwell/asym ratio (that is only needed
if it also has to create the fieldmap in rad/s internally).
So your command looks fine.
If your fieldmap extends to cover the whole brain then it doesn't matter about the
masking. The main reason for needing a brain extracted magnitude image is to
make sure you only use valid portions of the fieldmap, and in the general pipeline
to try and register the fieldmap with the EPI.
If you are getting good results with this command though, then I think everything is fine.
All the best,
Mark
On 1 Feb 2012, at 15:38, andrew Persichetti wrote:
> I am running fugue from command line, and I am not certain that my input is correct:
> "fugue -i b0map/run1.nii.gz --dwell=.0005 --loadfmap=b0map/fieldmap_rads.nii.gz -u b0map/run1_unwarped.nii.gz --unwarpdir=y-"
>
> I have noticed that others include a mask of a stripped mag image, but when I do this it does not look right (blacked out image).
> In my command line I am specifying the dwell time but not the dwell/asym ratio. do I need to do that, or is dwell fine?
>
> Overall, the images look good, but I just want to make sure that I haven't missed something.
>
> Thanks in advance for your help!
>
> Best,
> Andrew
>
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