hierakonpolis / mu-net Goto Github PK

Hi Riccardo De Feo,

I tried to run your MU-Net on some mouse T1-w images, but I couldn't get the skull stripping and segmentation results. The input file hasn't been overwritten.

The command I used is: python3 runMU-Net.py path/to/input/image --overwrite True

Then I got the following log info:

I noticed that the MU-Net is trained from a bunch of mouse T-2w images, would my T-1w input image be a problem? Besides, I don't understand the warning message and I didn't find any flag in the usage documentation that is relevant to specify the term, brain volume for sample.

Thanks for your time in advance!

Hi,

I have been looking for a tool to generate masks for our T2 RARE mouse brain data and haven't been successful in identifying any softwares that perform as described (typically, under segmenting areas while including lots of non-brain areas). I'm optimistic MU-Net could solve my need.

However, bounding box creation failed and therefore can't proceed. Example mouse nifti is linked below. Is it just an orientation issue compared to the trained model (basing this on the Jupyter notebook for training)?

Any help you can be would be terrific.

Thanks

https://arizona.box.com/s/xrnekw5tufxzi92grm0wt27xnq3evzog

We are interested in using your algorithm in our research. I successfully installed all the software as instructed, but I wasn't able to achieve any result. Could you please provide a bit more detailed instructions on how to run it. Thanks in advance!