oikosohn's Blog

You can download the CaPTk binary file  here .   cd ~/Downloads chmod +x CaPTk_1.9.0_Installer.bin # Specify the installation path with --target mkdir ~/CaPTk ./CaPTk_1.9.0_Installer.bin --target /home/$USER/CaPTk/ # Execute CaPTk GUI or double click CaPTk-1.9.0.bin cd ~/CaPTk/CaPTk/1.9.0 ./CaPTk-1.9.0.bin # Execute CaPTk CLI (Display BraTSPipeline, DeepMedic help information) /home/$USER/CaPTk/CaPTk/1.9.0/CaPTk-1.9.0.bin BraTSPipeline -h /home/$USER/CaPTk/CaPTk/1.9.0/CaPTk-1.9.0.bin DeepMedic -h

NVIDIA Graphics Driver, WSL2 and Docker for Windows Desktop must be installed to follow. Download Test NIfTI File I mounted C:\nsimg\fastsurfer\data on the docker container /data. The file will be located in /data/SubjectX in the docker container. curl -L https://github.com/neurolabusc/niivue-images/raw/main/chris_t1.nii.gz > C:\nsimg\fastsurfer\data\subjectX\chris_t1.nii.gz Run FastSurfer Docker container with GPU Instead of Linux user ID and group, you can enter numbers respectively. See this page for the rest of commands. I arbitrarily set it from --user$(id-u):$(id-g) to ---user 1000:1000 for running on Windows. docker run --gpus all -v C:\nsimg\fastsurfer\data:/data -v C:\nsimg\fastsurfer\output:/output -v C:\nsimg\fastsurfer\license:/fs_license --rm --user 1000:1000 deepmi/fastsurfer:latest --fs_license /fs_license/license.txt --t1 /data/subjectX/chris_t1.nii.gz --sid subjectX --sd /output

Docker Desktop for Windows, WSL2 must be installed to follow the practice below.  1.  Obtain a FreeSurfer License Key Obtain a license key from the FreeSurfer homepage . 2. Place license key I placed a license key in C:\nsimg\freesurfer 3. Create a Dockerfile # Pull cgvalle/freesurfer_vnc:latest  FROM cgvalle/freesurfer_vnc:latest    # Copy the license.txt to the docker's /root/freesurfer  COPY license.txt /root/freesurfer           4. Build an Image with Dockerfile Open a command prompt or powershell to run command below (in blue letter). You should build where Dockerfile and license.txt are. docker build -t fs_vnc . docker images 5. Run fs_vnc image as a container Run command below (in blue letters) at the command prompt or in the power shell. docker run -d --name fs_vnc -e VNC_PASSWORD=fsvnc -e SUBJECTS_DIR=/root/persistent/subjects -v C:\\nsimg\\freesurfer:/root/persistent -p 6080:80 -p 5900:5900 cgvalle/freesurfer_vnc:latest