MIC-DKFZ / HD-BET

MRI brain extraction tool
Apache License 2.0
262 stars 63 forks source link

Trouble installing on Mac OS X 10.13.6 #7

Closed Rad-dude closed 2 years ago

Rad-dude commented 4 years ago

Hi Fabian,

I was having trouble installing HD_BET. I'm on Mac OS X 10.13.6 ( this comes with a system python 2.7 ) so to setup with python 3 & pip3, I had to do so with conda virtual environment.

I used the "sudo -H install -e ." as when I ran the install command without the "sudo -H" I got the following warning: (Defaulting to user installation because normal site-packages is not writeable), and for some reason after the install, I simply couldn't find hd-bet or HD_BET on my path at all.

After a few attempts, I got it to work. Long story short, for Mac OS X, users will need a conda virtual environment with python3 and pip3 activated, then using "sudo -H pip install -e ." everything should be fine.

If the user attempts to install with "pip install -e ." or "pip install -e . --user", it still won't work. Also make sure to remove the previous attempts to install before going for the "sudo -H pip install -e ."

I thought this would be worth sharing for other Mac OS X users, although it is no longer an issue for me.

Thanks and best regards, AR

FabianIsensee commented 4 years ago

Hi there, thank you for sharing. I will update the Documentation accordingly soon. Best, Fabian

johnaeanderson commented 4 years ago

Hi Fabian,

Any chance those of us with macs could use opencl instead of cuda to accelerate the estimates?

thanks for the software!

FabianIsensee commented 4 years ago

Hi John, unfortunately this is not something that can be done easily, as it would require pytorch (which is the framework we use for GPU acceleration) to support opencl. I know that there is a branch for ROCm support (which is AMD's implementation of GPU acceleration) somewhere, but getting this to run will certainly be a lot of headaches (I tried just for fun a while ago). Best, Fabian

FabianIsensee commented 2 years ago

Thanks @m416kar98k