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SCIInstitute / Seg3D

Seg3D is a free volume segmentation and processing tool developed by the NIH Center for Integrative Biomedical Computing at the University of Utah Scientific Computing and Imaging (SCI) Institute.
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tool for combining volumes into single grid #89

Open jessdtate opened 9 years ago

jessdtate commented 9 years ago

I would like to have a tool to combine volumes. Often, clinical scans are acquired in multiple volumes, and we need to combine them. currently, this is tricky to do in Seg3D, and not perfect in SCIRun. The way I do it now is to pad one of the volumes (using a padding python script similar to what issue #75 would do), cropping the volume to the desired size, then using the resample tool to map the data onto the grid. This could be done in the python script using the resample tool.

a-y-khan commented 9 years ago

It would be helpful to see before and after images. Also, how do you do this in SCIRun?

jessdtate commented 9 years ago

In scirun, we use join fields, then map the volumes onto a latvol. This mostly works, however it doesn't handle overlapping data very well and it can be hard to choose the right grid size.

With a good padding tool (one that can pad in each direction independently (6 directions)), would go a long way to enabling similar functionality with the arithmetic and resampling tool.

jessdtate commented 9 years ago

Here are some images that will hopefully help.

before combine_before

after combine_after

jessdtate commented 9 years ago

I will probably write a python script that will do this. I will share it when I do.

jessdtate commented 7 years ago

Here is the script that I mentioned.

Combine_volumes.py.zip