Hi,
That looks perfectly normal to me.
I'm guessing that the registration of the fieldmap to the EPI is failing and hence your
EF_UD_warp is not actually in the right space. At this point it is probably easier if
you send us your data. You can do this via our upload site:
http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
and make sure you send us the reference number.
Hopefully we can sort it out easily.
All the best,
Mark
On 8 Mar 2011, at 17:11, Tyler Blazey wrote:
> Hi Mark,
>
> Thanks for your quick reply. Looking at the shift map in fslview, it does look like most of the voxels were only shifted by 1 or two voxels (I also confirmed by looking at the mean shift using fslstats). However, around the frontal pole/ medial prefrontal cortex, the shift ranges from 15 to 20 voxels. I have attached a screenshot from fslview that shows this (min .0001, max 15). Also I realized that I forgot to mention in my last message that I unwarping a DTI acquisition. I am not sure how relevant this is, but I thought I should mention it.
>
> As for the commands I am running to warp my mask I have tried the following:
>
> applywarp -i EF_D_example_func_mask -r EF_D_example_func_mask -o EF_UD_example_func_mask -w EF_UD_warp --interp=nn
>
> and
>
> applywarp -i EF_D_example_func_mask -r EF_D_example_func_mask -o EF_UD_example_func_mask -w EF_UD_warp --interp=trilinear.
>
> Thanks again for all you help.
>
> - Tyler
> <shift_screen.jpg>
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