Hoffman2:Software Tools:FastSurfer: Difference between revisions
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===FastSurfer=== | ===FastSurfer=== | ||
This current version requires CentOS 7 work | [https://github.com/Deep-MI/FastSurfer/ Official Website] | ||
This current version requires [https://www.ccn.ucla.edu/wiki/index.php/Hoffman2:Software_Tools:CentOS_7#CCN_modules_for_CentOS_7| CentOS 7]work nodes and conda environment. | |||
module load anaconda3/2020.11 | module load anaconda3/2020.11 | ||
. /u/local/apps/anaconda3/2020.11/etc/profile.d/conda.sh | . /u/local/apps/anaconda3/2020.11/etc/profile.d/conda.sh | ||
Use it with GPU node | |||
conda activate /u/project/CCN/apps/fastsurfer/202102_gpu | conda activate /u/project/CCN/apps/fastsurfer/202102_gpu | ||
Use it with regular CPU only node | |||
conda activate /u/project/CCN/apps/fastsurfer/202102_cpu | conda activate /u/project/CCN/apps/fastsurfer/202102_cpu | ||
FastSurfer code is under | |||
cd /u/project/CCN/apps/fastsurfer/202102/FastSurfer | cd /u/project/CCN/apps/fastsurfer/202102/FastSurfer | ||
To check the usage | To check the usage | ||
./run_fastsurfer.sh -h | ./run_fastsurfer.sh -h | ||
Once you finish using it, exit the conda virtual environment by | Once you finish using it, exit the conda virtual environment by | ||
conda deactivate | conda deactivate | ||
Latest revision as of 22:23, 16 August 2021
FastSurfer
This current version requires CentOS 7work nodes and conda environment.
module load anaconda3/2020.11 . /u/local/apps/anaconda3/2020.11/etc/profile.d/conda.sh
Use it with GPU node
conda activate /u/project/CCN/apps/fastsurfer/202102_gpu
Use it with regular CPU only node
conda activate /u/project/CCN/apps/fastsurfer/202102_cpu
FastSurfer code is under
cd /u/project/CCN/apps/fastsurfer/202102/FastSurfer
To check the usage
./run_fastsurfer.sh -h
Once you finish using it, exit the conda virtual environment by
conda deactivate