Hello,
I am pretty new to FSL and want to preprocess structural (t2/t1) and DTI
data for TBSS analysis. As I don`t know where and why the problem occurs I`d
like to shortly describe the steps I have taken so far:
1.eddy corrected DTI data
2.Cut out the first (unweighted B0) image
3.Register this B0 to T2
4.Register T2 to T1
5.assemble the resulting matrices in concatxfm
6.Apply Flirt Transformation with the result of „5.“, all 11 (1B0 + 10
B1000) DTI images as input and the B0 as reference.
The resulting images are blurred and incorrectly oriented. In step 3. and 4.
I already used the option „images incorrectly oriented“ for Flirt, otherwise
the result of the B0 to T2 registration was also incorrectly oriented. The
resulting images were correct, the problem in step 6 nevertheless occurred.
(Through trial and error I already noticed that this problem does not occur
if I make use of the „Identity Transformation“ in Flirt, therefore I
consider, that the matrices might still be based on the incorrectly oriented
image.)
What is also striking is that the structural images were shown in horizontal
slices in the top left of FSLView whereas the diffusion data showed the
sagittal slice in the top left. The orientation of the initial structural
and DTI images was correct, whereas the orientation was not correct on the
blurred and distorted images (result of 6.) .
Do you have any suggestions?
Thanks for your help,
Philip
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