From 65145143949b654d7af3f3943d8b7b20e1414255 Mon Sep 17 00:00:00 2001 From: lipsia-fmri Date: Fri, 19 Jul 2024 15:17:56 +0200 Subject: [PATCH 1/3] first commit --- recipes/lipsia/README.md | 21 +++++++++++++++++++++ recipes/lipsia/build.sh | 28 ++++++++++++++++++++++++++++ recipes/lipsia/test.sh | 0 3 files changed, 49 insertions(+) create mode 100644 recipes/lipsia/README.md create mode 100644 recipes/lipsia/build.sh create mode 100644 recipes/lipsia/test.sh diff --git a/recipes/lipsia/README.md b/recipes/lipsia/README.md new file mode 100644 index 00000000..5aabb25b --- /dev/null +++ b/recipes/lipsia/README.md @@ -0,0 +1,21 @@ + +---------------------------------- +## REPLACE_WITH_Name_of_Container/toolVersion ## +Short_description_of_container + +Example: +``` +``` + +More documentation can be found here: link_to_documentation + +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: +``` + +``` + +License: + +---------------------------------- diff --git a/recipes/lipsia/build.sh b/recipes/lipsia/build.sh new file mode 100644 index 00000000..a9118619 --- /dev/null +++ b/recipes/lipsia/build.sh @@ -0,0 +1,28 @@ +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 ${mountPointList}" \ + --workdir /opt \ + --install wget git curl ca-certificates unzip \ + --env PATH='$PATH':/opt/${toolName}-${toolVersion}/bin \ + --env DEPLOY_PATH=/opt/${toolName}-${toolVersion}/bin/ \ + --copy README.md /README.md \ + --copy test.sh /test.sh \ + --run="bash /test.sh" \ + > ${imageName}.${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 From 8d4bed9627d91c34b81c064755579f5530e79ef8 Mon Sep 17 00:00:00 2001 From: Gabriele Lohmann Date: Fri, 19 Jul 2024 15:30:56 +0200 Subject: [PATCH 2/3] first build attempt --- recipes/lipsia/build.sh | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/recipes/lipsia/build.sh b/recipes/lipsia/build.sh index a9118619..b1771fd3 100644 --- a/recipes/lipsia/build.sh +++ b/recipes/lipsia/build.sh @@ -15,14 +15,16 @@ neurodocker generate ${neurodocker_buildMode} \ --run="chmod +x /usr/bin/ll" \ --run="mkdir -p ${mountPointList}" \ --workdir /opt \ - --install wget git curl ca-certificates unzip \ - --env PATH='$PATH':/opt/${toolName}-${toolVersion}/bin \ - --env DEPLOY_PATH=/opt/${toolName}-${toolVersion}/bin/ \ + --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 \ - --copy test.sh /test.sh \ - --run="bash /test.sh" \ > ${imageName}.${neurodocker_buildExt} + if [ "$1" != "" ]; then ./../main_build.sh fi From 3b77bbcb7838389f9b688257a4c264a467c1f289 Mon Sep 17 00:00:00 2001 From: Gabriele Lohmann Date: Fri, 19 Jul 2024 15:35:36 +0200 Subject: [PATCH 3/3] added readme --- recipes/lipsia/README.md | 32 ++++++++++++++++++++++++++++---- 1 file changed, 28 insertions(+), 4 deletions(-) diff --git a/recipes/lipsia/README.md b/recipes/lipsia/README.md index 5aabb25b..c5f95348 100644 --- a/recipes/lipsia/README.md +++ b/recipes/lipsia/README.md @@ -1,21 +1,45 @@ ---------------------------------- -## REPLACE_WITH_Name_of_Container/toolVersion ## -Short_description_of_container +## 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: link_to_documentation +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: +License: BSD-3-Clause license + ----------------------------------