diff --git a/recipes/lipsia/README.md b/recipes/lipsia/README.md new file mode 100644 index 00000000..c5f95348 --- /dev/null +++ b/recipes/lipsia/README.md @@ -0,0 +1,45 @@ + +---------------------------------- +## 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 + + +---------------------------------- diff --git a/recipes/lipsia/build.sh b/recipes/lipsia/build.sh new file mode 100644 index 00000000..b1771fd3 --- /dev/null +++ b/recipes/lipsia/build.sh @@ -0,0 +1,30 @@ +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 diff --git a/recipes/lipsia/test.sh b/recipes/lipsia/test.sh new file mode 100644 index 00000000..e69de29b