Sorry, I was confused.
Thank you very much!
在 2012-12-2,上午12:10,Jesper Andersson <[log in to unmask]> 写道:
> 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
>
>
>>
>>
>> 在 2012-12-1,下午8:44,Mark Jenkinson <[log in to unmask]> 写道:
>>
>>> 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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