Hello,
The data were acquired on a GE 3T MR750 running DV22. We were surprised by the issue and happy to find a solution, but wanted to make sure it was appropriate.
Aaron D. Jacobson
Technical Operations Manager
UCSD Center for Functional MRI
9500 Gilman Drive
La Jolla CA 92093-0677
On 1/25/17, 9:21 AM, "FSL - FMRIB's Software Library on behalf of Harms, Michael" <[log in to unmask] on behalf of [log in to unmask]> wrote:
Hi,
What scanner was the data acquired on? We collected all the fMRI and dMRI
for HCP on Siemens with an oblique slice prescription, and didn’t have any
issues with a zipper artifact while using just 1’s/0’s in the topup
parameters file.
cheers,
-MH
--
Michael Harms, Ph.D.
-----------------------------------------------------------
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO 63110Email: [log in to unmask]
On 1/25/17, 10:55 AM, "FSL - FMRIB's Software Library on behalf of Aaron
Jacobson" <[log in to unmask] on behalf of [log in to unmask]> wrote:
Recently I ran into some issues using fsl topup on several oblique EPI
datasets. The topup corrected output had what looked like a zipper
artifact throughout many of the slices. I found that if I used 3dWarp
-deoblique prior to running the topup correction the artifact disappeared
(most of the time) but I was not confident that this method did not affect
my dataset in other ways. I found that if I used the REL image orientation
info from the dicom header (a measure of obliquity in the dataset) in the
my_acquisition_parameters file that is fed into the topup commands, the
corrected data look great.
Example from dicom header:
REL Image Orientation (Patient)//1\-0\0\-0\0.975766\-0.21881
Example of my_acquisition_parameters file:
0.21881 -0.975766 0 1
0.21881 -0.975766 0 1
-0.21881 0.975766 0 1
-0.21881 0.975766 0 1
Is it appropriate (or necessary) to use measures of obliquity from the
dicom header as input for the x and y columns in the
my_acquisition_parameters file? Should topup be able to handle oblique
datasets without setting the parameters in this way?
Any advice you can offer would be greatly appreciated.
Thanks!
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