docs/changes/newsfragments/342.misc

@@ -0,0 +1 @@
+Add support for accessing FreeSurfer via Docker wrapper along with ``mri_binarize``, ``mri_pretess``, ``mri_mc`` and ``mris_convert`` by `Synchon Mandal`_

docs/installation.rst

@@ -163,3 +163,36 @@ Or, alternatively, you can execute this command which will update the
 .. code-block:: bash
 
   junifer setup ants-docker | grep "PATH=" | xargs | >> ~/.bashrc
+
+FreeSurfer
+----------
+
+To install FreeSurfer, you can always follow the `FreeSurfer official instructions
+<https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall>`_. Additionally, you can
+also follow the following steps to install and configure the FreeSurfer Docker container
+in your local system.
+
+1. Install Docker. You can follow the
+   `Docker official instructions <https://docs.docker.com/get-docker/>`_.
+2. Pull the FreeSurfer Docker image from
+   `Docker Hub FreeSurfer <https://hub.docker.com/r/freesurfer/freesurfer>`_:
+
+.. code-block:: bash
+
+  docker pull freesurfer/freesurfer
+
+3. Add the Junifer FreeSurfer scripts to your PATH environment variable. Run the
+   following command:
+
+.. code-block:: bash
+
+  junifer setup freesurfer-docker
+
+Take the last line and copy it to your ``.bashrc`` or ``.zshrc`` file.
+
+Or, alternatively, you can execute this command which will update the
+``~/.bashrc`` for you:
+
+.. code-block:: bash
+
+  junifer setup freesurfer-docker | grep "PATH=" | xargs | >> ~/.bashrc

junifer/api/cli.py

@@ -588,3 +588,29 @@ def ants_docker() -> None:  # pragma: no cover
     export PATH="$PATH:{ants_wrappers_path}"
     """
     click.secho(msg, fg="blue")
+
+
+@setup.command("freesurfer-docker")
+def freesurfer_docker() -> None:  # pragma: no cover
+    """Configure FreeSurfer-Docker wrappers."""
+    import junifer
+
+    pkg_path = Path(junifer.__path__[0])  # type: ignore
+    fs_wrappers_path = pkg_path / "api" / "res" / "freesurfer"
+    msg = f"""
+    Installation instructions for FreeSurfer-Docker wrappers:
+
+    1. Install Docker: https://docs.docker.com/get-docker/
+
+    2. Get the FreeSurfer-Docker image by running this on the command line:
+
+        docker pull freesurfer/freesurfer
+
+    3. Get license from: https://surfer.nmr.mgh.harvard.edu/registration.html .
+       You can skip this step if you already have one.
+
+    4. Add this line to the ~/.bashrc or ~/.zshrc file:
+
+    export PATH="$PATH:{fs_wrappers_path}"
+    """
+    click.secho(msg, fg="blue")

junifer/api/res/freesurfer/mri_binarize

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+run_freesurfer_docker.sh mri_binarize "$@"

junifer/api/res/freesurfer/mri_mc

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+run_freesurfer_docker.sh mri_mc "$@"

junifer/api/res/freesurfer/mri_pretess

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+run_freesurfer_docker.sh mri_pretess "$@"

junifer/api/res/freesurfer/mris_convert

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+run_freesurfer_docker.sh mris_convert "$@"

junifer/api/res/freesurfer/run_freesurfer_docker.sh

@@ -0,0 +1,61 @@
+#!/bin/bash
+
+corrected_args=()
+docker_args=()
+mounts=0
+
+FS_LICENSE="${FS_LICENSE:=$HOME/freesurfer_license.txt}"
+
+if [ -f "${FS_LICENSE}" ]; then
+    >&2 echo "Using freesurfer license from ${FS_LICENSE}"
+else
+    >&2 echo "Freesurfer license not found at ${FS_LICENSE}. You can either set FS_LICENSE to the path of the license file or place the license file at
+${FS_LICENSE}"
+    exit 1
+fi
+
+# Map the license path to the container by binding
+license_path=$(realpath "${FS_LICENSE}")
+license_path_fname=$(basename "${FS_LICENSE}")
+host_dir=$(dirname "${license_path}")
+((mounts+=1))
+container_dir="/data/mount_${mounts}"
+docker_args+=("-v ${host_dir}:${container_dir}")
+export DOCKERENV_FS_LICENSE=${container_dir}/${license_path_fname}
+
+for var in "$@"
+do
+if [ -d "${var}" ]; then
+        echo "$var is a directory" >&2
+        var=$(realpath "${var}")
+        host_dir=$(dirname "${var}")
+        ((mounts+=1))
+        container_dir="/data/mount_${mounts}"
+        docker_args+=("-v ${host_dir}:${container_dir}")
+        var=${container_dir}
+    elif [ -f "${var}" ] || [[ "${var}" == /* ]]; then
+        if [ -f "${var}" ]; then
+            echo "$var is a file" >&2
+            var=$(realpath "${var}")
+        else
+            echo "$var is a prefix" >&2
+        fi
+        fname=$(basename "${var}")
+        host_dir=$(dirname "${var}")
+        ((mounts+=1))
+        container_dir="/data/mount_${mounts}"
+        docker_args+=("-v ${host_dir}:${container_dir}")
+        var=${container_dir}/${fname}
+    fi
+    corrected_args+=("${var}")
+done
+
+echo "Docker args: ${docker_args[*]}" >&2
+echo "Corrected args for FreeSurfer: ${corrected_args[*]}" >&2
+
+cwd=$(pwd)
+cmd="docker run --rm ${docker_args[*]} -v ${cwd}:${cwd} -w ${cwd} freesurfer/freesurfer ${corrected_args[*]}"
+echo "Running command: ${cmd}" >&2
+${cmd}
+
+unset DOCKERENV_FS_LICENSE

junifer/pipeline/utils.py

@@ -37,7 +37,7 @@ def check_ext_dependencies(
         If ``name`` is mandatory and is not found.
 
     """
-    valid_ext_dependencies = ("afni", "fsl", "ants")
+    valid_ext_dependencies = ("afni", "fsl", "ants", "freesurfer")
     if name not in valid_ext_dependencies:
         raise_error(
             "Invalid value for `name`, should be one of: "
@@ -52,6 +52,9 @@ def check_ext_dependencies(
     # Check for ants
     elif name == "ants":
         found = _check_ants(**kwargs)
+    # Check for freesurfer
+    elif name == "freesurfer":
+        found = _check_freesurfer(**kwargs)
 
     # Check if the dependency is mandatory in case it's not found
     if not found and not optional:
@@ -245,3 +248,63 @@ def _check_ants(commands: Optional[List[str]] = None) -> bool:
                 f"{commands_found_results}"
             )
     return ants_found
+
+
+def _check_freesurfer(commands: Optional[List[str]] = None) -> bool:
+    """Check if FreeSurfer is present in the system.
+
+    Parameters
+    ----------
+    commands : list of str, optional
+        The commands to specifically check for from FreeSurfer. If None, only
+        the basic FreeSurfer help would be looked up, else, would also
+        check for specific commands (default None).
+
+    Returns
+    -------
+    bool
+        Whether FreeSurfer is found or not.
+
+    """
+    completed_process = subprocess.run(
+        "recon-all -help",
+        stdin=subprocess.DEVNULL,
+        stdout=subprocess.DEVNULL,
+        stderr=subprocess.STDOUT,
+        shell=True,  # is unsafe but kept for resolution via PATH
+        check=False,
+    )
+    fs_found = completed_process.returncode == 0
+
+    # Check for specific commands
+    if fs_found and commands is not None:
+        if not isinstance(commands, list):
+            commands = [commands]
+        # Store command found results
+        commands_found_results = {}
+        # Set all commands found flag to True
+        all_commands_found = True
+        # Check commands' existence
+        for command in commands:
+            command_process = subprocess.run(
+                [command],
+                stdin=subprocess.DEVNULL,
+                stdout=subprocess.DEVNULL,
+                stderr=subprocess.STDOUT,
+                shell=True,  # is unsafe but kept for resolution via PATH
+                check=False,
+            )
+            command_found = command_process.returncode == 0
+            commands_found_results[command] = (
+                "found" if command_found else "not found"
+            )
+            # Set flag to trigger warning
+            all_commands_found = all_commands_found and command_found
+        # One or more commands were missing
+        if not all_commands_found:
+            warn_with_log(
+                "FreeSurfer is installed but some of the required commands "
+                "were not found. These are the results: "
+                f"{commands_found_results}"
+            )
+    return fs_found