Content Comparison

Install WSL

Use latest release of Ubuntu

(May not be needed) Set default user to be root (make life simpler with permissions): Start PowerShell => C: => ubuntu config --default-user root (details)

Open linux shell - Ubuntu app in Windows

Install conda

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh

You have to view then agree to terms, then run install responding to various questions

Install ANTs

conda create -n antsenv -c conda-forge ants -y   # create env and install ANTs
conda activate antsenv

Note: all sessions need to start with “conda activate antsenv” to access ANTs

Install FSL in same environment

In Ubuntu shell

  # Go into ANTs environment
conda activate antsenv                 # <- your ANTs env is now on $PATH
  # Download the installer
wget -O fslinstaller.py https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py
  # Run the installation
python3 fslinstaller.py --conda --prefix "$CONDA_PREFIX"

Important! When it asks: Where do you want to install FSL? [/usr/local/fsl/]:

type $CONDA_PREFIX/fsl

Image Added

Now we need to set the initailization to point to fsl (in this “antsenv” environment)

conda activate antsenv

cat > "$CONDA_PREFIX/etc/conda/activate.d/fsl.sh" <<'EOF'
export FSLDIR="${CONDA_PREFIX}/fsl"
source "${FSLDIR}/etc/fslconf/fsl.sh" >/dev/null
EOF

# ---------- deactivate ----------
cat > "$CONDA_PREFIX/etc/conda/deactivate.d/fsl.sh" <<'EOF'
# remove FSL from PATH and tidy
if command -v pathremove &>/dev/null; then
    pathremove "${FSLDIR}/bin"
fi
unset FSLDIR
EOF

These folders will be created (no need to create them):

(antsenv) root@REDWSONFAC26495:~# mkdir ~/rats_mri_project/
(antsenv) root@REDWSONFAC26495:~# cd rats_mri_project/
(antsenv) root@REDWSONFAC26495:~/rats_mri_project# mkdir template
(antsenv) root@REDWSONFAC26495:~/rats_mri_project# mkdir priors
(antsenv) root@REDWSONFAC26495:~/rats_mri_project# mkdir subjects
(antsenv) root@REDWSONFAC26495:~/rats_mri_project# mkdir outputs