How to create MIP images from the command line?

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1

Hello Dear Developers and Users

Can the MIP viewer module be run from the command line?
In other words, how can I generate axial MIP images from the command line by setting Slice Size MIP in any way possible?

Please guide me.
Thanks a lot.
Shahrokh.

2

Hello @shahrokh

One option is to write a python script to generate the MIP and write out the resliced image output to a file.

https://www.slicer.org/wiki/Documentation/Nightly/ScriptRepository#Thick_slab_reconstruction_and_maximum.2Fminimum_intensity_volume_projections

You can then run your python script using --python-script command line option in Slicer.

-Andinet

1 Like
3

Hello Andinet

Thank you very much for your guidance. I have some questions about the concept of MIP that I hope you will guide me, perhaps I should not ask my question in here.

Thanks a lot for your help. To create the MIP images, I used the Python code provided on github:
Title: GitHub - ljpadam/maximum_intensity_projection: Maximum intensity projection for medical image
Address: GitHub - ljpadam/maximum_intensity_projection: Maximum intensity projection for medical image

I think that the slices_num parameter in the maximum_intensity_projection.py code (in the above link) is similar to the Slice size MIP in the module of MIP Viewer. Is it true?

As you can see in the following image, if I increase slices_num in the code of maximum_intensity_projection.py or Slice Size MIP in 3DSlicer, more arteries will be projected in the axial slice.

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This destroys the vascular view in the coronal slice as you can see in the following image:

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Is this situation unavoidable in a MIP view?

How can I have good quality of MIPs in the three directions (AP, IS and LR)?

Please guide me.
Thanks a lot.
Shahrokh.

4

This code, as is, does not make a lot of sense, as it does thick slice reformat for every slice of a volume. However, you could easily change it to compute the maximum intensity for all slices and along any of the 3 images axes.

If you need arbitrarily oriented views then I would recommend to use the script that @Andinet_Enquobahrie linked above. If you need perspective projection (to simulate fluoroscopy images) or you need fast MIP generation (50-100 images per second) and 8 bit precision is enough then you can use the volume renderer.