From b2d0f521f1381701711ed5ae0e6b49132b6e5dfa Mon Sep 17 00:00:00 2001
From: Joshua Scarsbrook <jscarsbrook@gmail.com>
Date: Thu, 12 Sep 2024 18:53:57 +1000
Subject: [PATCH] Added synthstrip 7.4.1

---
 recipes/synthstrip/README.md       | 15 +++++++++++
 recipes/synthstrip/build.sh        | 37 +++++++++++++++++++++++++++
 recipes/synthstrip/synthstrip.star | 41 ++++++++++++++++++++++++++++++
 3 files changed, 93 insertions(+)
 create mode 100644 recipes/synthstrip/README.md
 create mode 100755 recipes/synthstrip/build.sh
 create mode 100644 recipes/synthstrip/synthstrip.star

diff --git a/recipes/synthstrip/README.md b/recipes/synthstrip/README.md
new file mode 100644
index 00000000..862ad23f
--- /dev/null
+++ b/recipes/synthstrip/README.md
@@ -0,0 +1,15 @@
+
+----------------------------------
+## synthstrip/toolVersion##
+
+SynthStrip is a skull-stripping tool that extracts brain voxels from a landscape of image types, ranging across imaging modalities, resolutions, and subject populations. It leverages a deep learning strategy to synthesize arbitrary training images from segmentation maps, yielding a robust model agnostic to acquisition specifics.
+
+**Citation:** SynthStrip: Skull-Stripping for Any Brain Image Andrew Hoopes, Jocelyn S. Mora, Adrian V. Dalca, Bruce Fischl*, Malte Hoffmann* (*equal contribution) NeuroImage 260, 2022, 119474 https://doi.org/10.1016/j.neuroimage.2022.119474
+
+**Homepage:** https://surfer.nmr.mgh.harvard.edu/docs/synthstrip/
+
+**Example:** `mri_synthstrip`
+
+**License:** FreeSurfer Software License Agreement
+
+----------------------------------
diff --git a/recipes/synthstrip/build.sh b/recipes/synthstrip/build.sh
new file mode 100755
index 00000000..b935f8ee
--- /dev/null
+++ b/recipes/synthstrip/build.sh
@@ -0,0 +1,37 @@
+#!/usr/bin/env bash
+set -e
+
+export toolName='synthstrip'
+export toolVersion='7.4.1'
+
+if [ "$1" != "" ]; then
+    echo "Entering Debug mode"
+    export debug=$1
+fi
+
+source ../main_setup.sh
+
+# Use Singlrity/Apptainer to run TinyRange to generate the rootfs.
+singularity run -B /storage:/storage docker://ghcr.io/tinyrange/tinyrange:stable build synthstrip.star:synthstrip_root -o synthstrip.tar
+
+# Make sure the automaticcly included template doesn't add to the final layer.
+neurodocker generate ${neurodocker_buildMode} \
+    --base-image ubuntu \
+    --pkg-manager apt \
+    --base-image scratch \
+    --add synthstrip.tar . \
+    --run "/init -run-scripts /.pkg/scripts.json" \
+    --run "/init -run-scripts /wheels/scripts.json" \
+    --run="printf '#!/bin/bash\nls -la' > /usr/bin/ll" \
+    --run="chmod +x /usr/bin/ll" \
+    --run="mkdir -p ${mountPointList}" \
+    --env FREESURFER_HOME=/freesurfer \
+    --run="ln -s /usr/bin/python3 /usr/bin/python" \
+    --entrypoint "/bin/bash" \
+    --env DEPLOY_BINS=mri_synthstrip \
+    --copy README.md /README.md \
+ > ${imageName}.${neurodocker_buildExt}
+
+if [ "$1" != "" ]; then
+   ./../main_build.sh
+fi
diff --git a/recipes/synthstrip/synthstrip.star b/recipes/synthstrip/synthstrip.star
new file mode 100644
index 00000000..e25fe119
--- /dev/null
+++ b/recipes/synthstrip/synthstrip.star
@@ -0,0 +1,41 @@
+load("//lib/pypi.star", "build_fs_for_requirements")
+
+requirements = "https://surfer.nmr.mgh.harvard.edu/docs/synthstrip/requirements/requirements.txt"
+
+files = [
+    "https://github.com/freesurfer/freesurfer/raw/v7.4.1/mri_synthstrip/mri_synthstrip",
+    "https://surfer.nmr.mgh.harvard.edu/docs/synthstrip/requirements/synthstrip.1.pt",
+    "https://surfer.nmr.mgh.harvard.edu/docs/synthstrip/requirements/synthstrip.nocsf.1.pt",
+]
+
+base = define.plan(
+    builder = "ubuntu@jammy",
+    packages = [
+        query("python3-pip"),
+        query("python3-packaging"),
+    ],
+    tags = ["level3", "defaults"],
+)
+
+requirements_fs = build_fs_for_requirements(base, define.fetch_http(requirements))
+
+def synthstrip_fs(ctx, script, data_1, data_2):
+    ret = filesystem()
+
+    ret["usr/bin/mri_synthstrip"] = file(script, executable = True)
+
+    ret["freesurfer/models/synthstrip.1.pt"] = data_1
+    ret["freesurfer/models/synthstrip.nocsf.1.pt"] = data_2
+
+    return ctx.archive(ret)
+
+synthstrip_root = define.build_fs([
+    base.set_tags([
+        "level3",
+        "defaults",
+        "noScripts",
+    ]),
+    requirements_fs,
+    define.build(synthstrip_fs, *[define.fetch_http(file) for file in files]),
+    directive.builtin("init", "/init"),
+], "tar")