Multi-component options unavailable in ITK-snap 4.X

[Carl Kulseng]

Hi i have noticed that I am no longer able to average the intensities in a 4D dynamic series, it is possible in 3.8.

Attached screenshots of both 3.8 and 4.0

[Jilei Hao]

Hi Carl,

It is by design in 4.0. 

In 3.8, 4D images were read as multi-component. That's why the 4th dimension can be averaged. But from 4.0, they are no longer read as multi-component images but as a single component 4D image. And itk-snap currently can only perform pixel-wise average on multi-component images. 

Best,

Jilei

On Tue, Aug 8, 2023 at 8:52 AM Carl Kulseng <carlk...@gmail.com> wrote:

Hi i have noticed that I am no longer able to average the intensities in a 4D dynamic series, it is possible in 3.8.

Attached screenshots of both 3.8 and 4.0

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[Carl]

Hi ok thank for the clarification. Actually, being able to average all the dynamic series together made the manual segmentation more effective in our case. So we will have to use 3.8 for that feature?

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[Paul Yushkevich]

Hi Carl,

You bring up a good point that others have brought up as well. We should add in the next release an option when loading a 4D image to treat it as a 3D multicomponent image as opposed to a 3D+time image. A work around for now would be to use a NIFTI library to reformat the image as a multi-component one. If I recall correctly, a 3D+time NIFTI with 256^3 voxels and 10 time points has dimensions [256,256,256,10,1] while a multi-component NIFTI with 10 components has dimensions [256,256,256,1,10], in which case it would be a short Python script to modify the image. Also can be done using c3d, 

I think this code

c3d -mcs your_image.nii.gz -omc your_image_mc.nii.gz

should load a 3D+time image and save as a 3D multi component. If not, then try:

c4d your_image.nii.gz -slice w 1:-1 -omc your_image_mc.nii.gz

Please let me know if that helps,

Paul

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[Jilei Hao]

That's right.

On Tue, Aug 8, 2023 at 1:00 PM Carl <carlk...@gmail.com> wrote:

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[Carl]

Hi Paul, hope you are doing well. The approach you mention works fine as a work-around. 

Thank you

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