From 9ab572f102bbbfb7914a3391f60e9ea3e87406dc Mon Sep 17 00:00:00 2001
From: Thom Shaw <31721414+thomshaw92@users.noreply.github.com>
Date: Fri, 27 Sep 2024 15:21:48 +1000
Subject: [PATCH] dcm2niix container recipe

---
 recipes/dcm2niix/README.md | 23 +++++++++++++++++++++++
 recipes/dcm2niix/build.sh  | 35 +++++++++++++++++++++++++++++++++++
 recipes/dcm2niix/test.sh   |  1 +
 3 files changed, 59 insertions(+)
 create mode 100644 recipes/dcm2niix/README.md
 create mode 100644 recipes/dcm2niix/build.sh
 create mode 100644 recipes/dcm2niix/test.sh

diff --git a/recipes/dcm2niix/README.md b/recipes/dcm2niix/README.md
new file mode 100644
index 00000000..3011aefb
--- /dev/null
+++ b/recipes/dcm2niix/README.md
@@ -0,0 +1,23 @@
+
+----------------------------------
+## dcm2niix/v1.0.20240202' ##
+dcm2niix is designed to convert neuroimaging data from the DICOM format to the NIfTI format. This web page hosts the developmental source code - a compiled version for Linux, MacOS, and Windows of the most recent stable release is included with MRIcroGL. A full manual for this software is available in the form of a NITRC wiki.
+
+Example:
+```
+./dcm2niix ./test-dicom-dir -b y 
+```
+
+More documentation can be found here: (https://github.com/rordenlab/dcm2niix?tab=readme-ov-file)
+
+To make the executables and scripts inside this container transparently available in the command line of environments where Neurocommand is installed: ml dcm2niix/v1.0.20240202
+
+Citation:
+```
+Li X, Morgan PS, Ashburner J, Smith J, Rorden C (2016) The first step for neuroimaging data analysis: DICOM to NIfTI conversion. J Neurosci Methods. 264:47-56. doi: 10.1016/j.jneumeth.2016.03.001. PMID: 26945974
+```
+
+License: This software is open source. The bulk of the code is covered by the BSD license. Some units are either public domain (nifti*.*, miniz.c) or use the MIT license (ujpeg.cpp). See the license.txt file for more details.
+https://github.com/rordenlab/dcm2niix/blob/master/license.txt
+
+----------------------------------
diff --git a/recipes/dcm2niix/build.sh b/recipes/dcm2niix/build.sh
new file mode 100644
index 00000000..92e0c01f
--- /dev/null
+++ b/recipes/dcm2niix/build.sh
@@ -0,0 +1,35 @@
+#!/usr/bin/env bash
+set -e
+
+export toolName='dcm2niix'
+export toolVersion='v1.0.20240202'
+
+# Don't forget to update version change in README.md!!!!!
+
+if [ "$1" != "" ]; then
+    echo "Entering Debug mode"
+    export debug=$1
+fi
+
+source ../main_setup.sh
+
+neurodocker generate ${neurodocker_buildMode} \
+    --base-image ubuntu:20.04 \
+    --pkg-manager apt \
+    --run="printf '#!/bin/bash\nls -la' > /usr/bin/ll" \
+    --run="chmod +x /usr/bin/ll" \
+    --run="mkdir -p ${mountPointList}" \
+    --install git wget ca-certificates pigz \
+    --workdir /opt/${toolName}-${toolVersion} \
+    --run="curl -fLO https://github.com/rordenlab/dcm2niix/releases/latest/download/dcm2niix_lnx.zip \
+        && unzip dcm2niix_lnx.zip \
+        && chmod a+rwx /opt/${toolName}-${toolVersion}/${toolName} \
+        && rm -rf dcm2niix_lnx.zip" \
+    --env PATH='$PATH':/opt/${toolName}-${toolVersion} \
+    --env DEPLOY_PATH=/opt/${toolName}-${toolVersion} \
+    --copy README.md /README.md \
+> ${imageName}.${neurodocker_buildExt}
+
+if [ "$1" != "" ]; then
+    ./../main_build.sh
+fi
\ No newline at end of file
diff --git a/recipes/dcm2niix/test.sh b/recipes/dcm2niix/test.sh
new file mode 100644
index 00000000..68a155c1
--- /dev/null
+++ b/recipes/dcm2niix/test.sh
@@ -0,0 +1 @@
+dcm2niix 
\ No newline at end of file