Hi Ai,
> 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
you error is that you feed the --iout into applywarp. The --iout is already warped, which means you warp it twice. The --in to applywarp should be the same as the input to --in to fnirt.
Good luck Jesper
>
>
> 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.
>>>
>>>
>>>
>>>
>>>
>
|