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plmoer / skull_stripping_code_SR

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Is the preprocessing pipeline available? #4

Open mariamonzon opened 1 year ago

mariamonzon commented 1 year ago

Thanks a lot for the great contribution :-)

In the paper and in the code you specify the preprocessing pipeline. Is this also contained in the repository? The comments reference to test_raw.py but I cannot find it in the code.

Thanks in advance!

plmoer commented 1 year ago

The preprocessing code is in the file of loadFusionImage.py. The comment reference to test_raw.py was obsolete. I combined the work in the file of test_online.py

mariamonzon commented 1 year ago

Thanks so much!!

mariamonzon commented 1 year ago

Is also the full preprocessing pipeline also there?

plmoer commented 1 year ago

It only has the normalization part in the preprocessing pipeline. In my work, I used CBICA CaPTK (https://www.med.upenn.edu/cbica/captk/) for bias correction and Greedy (https://greedy.readthedocs.io) for co-registration. Command for co-registration: greedy -d 3 -a -m NMI -i $refPath $n4Path -o $aff1 -ia-image-centers -n 100x50x10 -dof 6 please check details at https://greedy.readthedocs.io/en/latest/reference.html#affine-and-rigid-registration.

I will release all preprocessing code sometime later. If have questions, I am happy to give advice.