Thank you, Mark.
Original data: LSM_MPR
Using fslroi to remove some of neck to get the image: LSM_MPR_roi
Using FLIRT GUI, DOF=12, input image is LSM_MPR_roi, ref MNI152_T1_2mm, and get the matrix file: LSM_MPR_roi_brain_flirt;
Then FNIRT:
fnirt --in=LSM_MPR_roi --aff=LSM_MPR_roi_brain_flirt.mat --config=/usr/local/fsl/etc/flirtsch/T1_2_MNI152_2mm.cnf --cout=coef_LSM_MPR_to_MNI152 --iout=LSM_MPR_fnirt_2mm --jacrange=0.01,100
applywarp --in=LSM_MPR_fnirt_2mm --out=LSM_MPR_fnirt --ref=/usr/local/fsl/data/standard/MNI152_T1_1mm --warp=coef_LSM_MPR_to_MNI152
ÔÚ 2012-12-1£¬ÏÂÎç8:44£¬Mark Jenkinson <[log in to unmask]> дµÀ£º
> 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,
>>
>> 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.
>>
>> 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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