Merge pull request #725 from lipsia-fmri/lipsia

recipes/lipsia/README.md

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+
+----------------------------------
+## lipsia/toolVersion ##
+
+
+Example:
+```
+*Onesample test at the 2nd level* (`vlisa_onesample`_). 
+Example: the input is a set of contrast maps called "data_*.nii.gz"::
+
+  vlisa_onesample -in data_*.nii.gz -mask mask.nii -out result.v
+  vnifti -in result.v -out result.nii
+
+
+*Twosample test at the 2nd level* (`vlisa_twosample`_). 
+Example: input are two sets of contrast maps called "data1_*.nii.gz" and "data2_*.nii.gz"::
+
+  vlisa_twosample -in1 data1_*.nii.gz -in2 data2_*.nii.gz -mask mask.nii -out result.v
+  vnifti -in result.v -out result.nii
+
+
+*Single subject test (1st level)* (`vlisa_prewhitening`_). 
+Example: input are two runs acquired in the same session called "run1.nii.gz" and "run2.nii.gz".
+Preprocessing should include a correction for baseline drifts!::
+
+
+  vlisa_prewhitening -in run1.nii.gz run2.nii.gz -design des1.txt des2.txt -mask mask.nii -out result.v 
+  vnifti -in result.v -out result.nii
+```
+
+More documentation can be found here:  https://github.com/lipsia-fmri/lipsia
+
+To make the executables and scripts inside this container transparently available in the command line of environments where Neurocommand is installed: ml REPLACE_WITH_Name_of_Container/toolVersion
+
+Citation:
+```
+Lohmann et al (2023) "Improving the reliability of fMRI-based predictions of intelligence via semi-blind machine learning", bioRxiv, https://doi.org/10.1101/2023.11.03.565485
+
+
+```
+
+License: BSD-3-Clause license 
+
+
+----------------------------------

recipes/lipsia/build.sh

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+export toolName='lipsia'
+export toolVersion='3.1.1' 
+
+if [ "$1" != "" ]; then
+    echo "Entering Debug mode"
+    export debug=$1
+fi
+source ../main_setup.sh
+
+neurodocker generate ${neurodocker_buildMode} \
+   --base-image ubuntu:18.04 \
+   --env DEBIAN_FRONTEND=noninteractive \
+   --pkg-manager apt \
+   --run="printf '#!/bin/bash\nls -la' > /usr/bin/ll" \
+   --run="chmod +x /usr/bin/ll" \
+   --run="mkdir -p ${mountPointList}" \
+   --workdir /opt \
+   --install wget git curl ca-certificates unzip build-essential libgsl0-dev libboost-dev zlib1g-dev git lsb-release libopenblas-dev \
+   --run="git clone --depth 1 --branch ${toolVersion} https://github.com/lipsia-fmri/lipsia.git \ 
+    	&& cd lipsia && bash -c \"source lipsia-setup.sh && cd src && make\"" \
+   --env PATH='$PATH':/opt/${toolName}/bin \
+   --env LD_LIBRARY_PATH='$LD_LIBRARY_PATH':/opt/${toolName}/lib \
+   --env DEPLOY_PATH=/opt/${toolName}/bin/ \
+   --copy README.md /README.md \
+  > ${imageName}.${neurodocker_buildExt}
+
+
+if [ "$1" != "" ]; then
+   ./../main_build.sh
+fi