Dear Dianne,

I assume this is the output you get directly from topup with the --iout?

It is a consequence of using a periodic boundary condition in the spline resampling and not masking the output before writing it to file. The --iout output i intended to give an idea of if the estimation has worked or not, so I wasn't as careful as I could have been when writing it.

The output that intended for subsequent use is the output of applytopup and that should not have this issue.

Jesper


On 18 May 2013, at 22:52, Dianne Patterson wrote:

Dear Group, 

I have applied topup each of several subjects and seen similar problems for each one.  In each case I put in a blip_up image consisting of 2 B0s and a blip_down image consisting of 2 B0s.  The images are acquired in an axial plane. I checked these images and there is no wrap around of the slices.

Topup produces an unwarped image that then seems to have one slice that is completely misplaced.  

In Case 1, I get the lowest slice through the cerebellum appearing at the top of the image: 

<image.jpeg>

In Case 2, I get a slice that looks like it has been sheared in half.  
<image.jpeg>

It does not seem to affect more than one slice....but I'm wondering if this behavior is to be expected?

Thanks, 

Dianne
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Dianne Patterson, Ph.D.
Research Scientist
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