[Vv] clitkCropImage behaviour

[Benoît Presles]

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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