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By default, the cpu-tensorflow package is installed, but if you're on a machine that allows it, you can use the gpu-enabled tensorflow by adding to the following search paths: By default, the gpu-tensorflow package is installed, and to use it, you must point to the CUDA libraries via LD_LIBRARY_PATH:
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export PYTHONPATH=/space/freesurfer/python/linux/tensorflow-gpu:$PYTHONPATH
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Keep in mind that '''/usr/pubsw/packages/CUDA/lib64''' contains the shared libraries for many cuda versions, so you should refrain from including it in LD_LIBRARY_PATH until you're actually using cuda, since it will slow down program launches by searching that whole network directory. Keep in mind that '''/usr/pubsw/packages/CUDA/lib64''' contains the shared libraries for many CUDA versions, so you should refrain from including it in LD_LIBRARY_PATH until you're actually using cuda, since it will slow down program launches by searching that whole network directory.

FreeSurfer Python Development

To facilitate straightforward and reproducible python development in the lab, a custom python3 (anaconda) distribution for internal developers is installed at /space/freesurfer/python/linux. To use this version, make sure all calls to python or python3 point to this install by adding the following to your PATH.

export PATH=/space/freesurfer/python/linux/bin:$PATH

Keep in mind there's also a python3 link in /usr/pubsw/bin, so it's important that /space/freesurfer/python/linux/bin comes before that in your PATH.

Developing and Using the FreeSurfer Python Library

The freesurfer python library, which contains general utilities and various submodules like deepsurfer, gems, and samseg, is developed in the repository under repo/python/freesurfer. In order to utilize this library during development, you must point your PYTHONPATH at it:

export PYTHONPATH=/path/to/your/freesurfer-repository/python:$PYTHONPATH

This allows you to import your working version of the freesurfer library in any script or python interpreter. You can test it by opening a python interpreter and running:

import freesurfer as fs
status = fs.run('echo hello!')

Tensorflow GPU

By default, the gpu-tensorflow package is installed, and to use it, you must point to the CUDA libraries via LD_LIBRARY_PATH:

export LD_LIBRARY_PATH=/usr/pubsw/packages/CUDA/lib64:$LD_LIBRARY_PATH

Keep in mind that /usr/pubsw/packages/CUDA/lib64 contains the shared libraries for many CUDA versions, so you should refrain from including it in LD_LIBRARY_PATH until you're actually using cuda, since it will slow down program launches by searching that whole network directory.

Python (last edited 2021-08-26 13:24:17 by AndrewHoopes)