Hi,
It is hard to help without knowing your exact commands.
Can you include them?
The problem of registering when one image contains a lot of neck is well know, and can be dealt with by either manually using fslroi like you are doing, or by using robustfov.
All the best,
Mark
On 1 Dec 2012, at 10:23, Ai Qing <[log in to unmask]> wrote:
> Dear FSL experts,
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> I found FLIRT does not work normally in some MPRAGE images. These images often include much range of spinal cord. When I remove the some spinal cord image using fslroi(smaller range of coordination Y), FLIRT become normal. But FNIRT(1mm) does not work normally.
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> My data is MPRAGE, voxel sieze 1*1*1m^3; first FLIRT to 2mm, then FNIRT to 2mm, and using applywarp to FNIRT to 1mm. Images of FNIRT_2mm looks like not bad, but FNIRT_1mm distort obviously.
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