[Vv] clitkCropImage behaviour

[Benoît Presles]

Hello Thomas,

I have tried the tool with your update and there is no more bugs :-)
Thanks for your help.

Best regards,
Ben


Le 15/11/2018 à 17:08, Thomas BAUDIER a écrit :
> 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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