[Vv] clitkCropImage behaviour

[Thomas BAUDIER]

Hi Benoit,

I investigated and you right, the behavior of the tool is different with 
and without like option.
I did modifications 
(https://github.com/open-vv/vv/commit/05e26237e30a14a226cb4eb480a0eb9697f8ba06) 
and now the output is registered with the input. I add the option 
updateOrigin to have the previous behavior.

Regards
Thomas


On 2018-11-14 08:03, Benoît Presles wrote:
> Dear Thomas,
> 
> Do you still think that clitkCropImage has the good behavior?
> To keep the images registered, I think that WB_crop.nii should not
> have the same origin as WB_CTAC.nii but should have the same origin as
> ROI_1_tumeur_autocrop.nii.
> 
> Best regards,
> Ben
> 
> 
>> Le 9 nov. 2018 à 19:20, Benoît Presles <benoit.presles at u-bourgogne.fr> 
>> a écrit :
>> 
>> Hi Thomas,
>> 
>> To be exhaustive, here is what I do. I have two input images 
>> WB_CTAC.nii (double image) and ROI_1_tumeur.nii (binary image).
>> They have the same size, same spacing and same origin and are 
>> registered.
>> 
>> First I autocrop the ROI_1_tumeur.nii image thanks to the 
>> clitkAutoCrop tool:
>> clitkAutoCrop -i ROI_1_tumeur.nii -o ROI_1_tumeur_autocrop.nii.
>> 
>> After this first step, ROI_1_tumeur_autocrop.nii has a new size and a 
>> new origin and/but it is registered with ROI_1_tumeur.nii and 
>> WB_CTAC.nii.
>> 
>> Then, I do: clitkCropImage -i WB_CTAC.nii -o WB_crop.nii 
>> --like=ROI_1_tumeur_autocrop.nii -v
>> 
>> After this last step, WB_crop.nii has the same size as 
>> ROI_1_tumeur_autocrop.nii but has the same origin as WB_CTAC.nii, 
>> therefore WB_crop.nii is not aligned/registered with WB_CTAC.nii and 
>> ROI_1_tumeur_autocrop.nii.
>> 
>> 
>> Should I proceed differently ?
>> 
>> 
>> Thanks for your help,
>> Best regards,
>> Ben
>> 
>> 
>> 
>>> Le 09/11/2018 à 15:58, Thomas BAUDIER a écrit :
>>> 
>>> Hi Benoit,
>>> 
>>> Usually, this crop tool is used when you have 2 overlayed images. And 
>>> we cropped one image using the size of the second image. So we need 
>>> to change the origin to keep the registration OK.
>>> 
>>> Maybe if you really need a crop without the origin modification, I 
>>> can try to add an option (eg: --nooriginmodification)
>>> 
>>> Regards
>>> Thomas
>>> 
>>> 
>>>> On 2018-11-08 18:16, Benoît Presles wrote:
>>>> Dear vv users,
>>>> 
>>>> I am using clitkCropImage but I am not sure that this tool has the
>>>> good behaviour.
>>>> When I execute this command line: clitkCropImage -i WB_CTAC.nii -o
>>>> WB_crop.nii --like=ROI_1_tumeur_autocrop.nii -v, the WB_crop image 
>>>> has
>>>> the same size as the ROI_1_tumeur_autocrop image but has the same
>>>> origin as the WB_CTAC image.
>>>> 
>>>> WB_crop should not have the same origin as the like image ?
>>>> 
>>>> 
>>>> Best regards,
>>>> Ben
>>>> 
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>> 
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