diff --git a/recipes/heudiconv/README.md b/recipes/heudiconv/README.md new file mode 100644 index 00000000..859d30fe --- /dev/null +++ b/recipes/heudiconv/README.md @@ -0,0 +1,22 @@ + +---------------------------------- +## heudiconv/1.3.1 ## +heudiconv is a flexible DICOM converter for organizing brain imaging data into structured directory layouts. + +Example: +``` +heudiconv --files dicom/219/itbs/*/*.dcm -o Nifti -f Nifti/code/heuristic1.py -s 219 -ss itbs -c dcm2niix -b --minmeta --overwrite +``` + +More documentation can be found here: https://heudiconv.readthedocs.io/en/latest/quickstart.html + +To make the executables and scripts inside this container transparently available in the command line of environments where Neurocommand is installed: ml heudiconv/1.3.1 + +Citation: +``` +Halchenko, Yaroslav O., Mathias Goncalves, Satrajit Ghosh, Pablo Velasco, Matteo Visconti Di Oleggio Castello, Taylor Salo, John T. Wodder Ii, et al. “HeuDiConv — Flexible DICOM Conversion into Structureddirectory Layouts.” Journal of Open Source Software 9, no. 99 (July 3, 2024): 5839. https://doi.org/10.21105/joss.05839. +``` + +License: Apache License, Version 2.0 + +---------------------------------- diff --git a/recipes/heudiconv/build.sh b/recipes/heudiconv/build.sh new file mode 100644 index 00000000..876d725b --- /dev/null +++ b/recipes/heudiconv/build.sh @@ -0,0 +1,26 @@ +export toolName='heudiconv' +export toolVersion='1.3.1' +# https://hub.docker.com/r/nipy/heudiconv/tags + +if [ "$1" != "" ]; then + echo "Entering Debug mode" + export debug=$1 +fi + +source ../main_setup.sh --reinstall_neurodocker=false + +neurodocker generate ${neurodocker_buildMode} \ + --base-image nipy/heudiconv:$toolVersion \ + --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}" \ + --env DEPLOY_BINS=heudiconv \ + --copy README.md /README.md \ + --copy test.sh /test.sh \ + > ${imageName}.${neurodocker_buildExt} + +if [ "$1" != "" ]; then + ./../main_build.sh +fi diff --git a/recipes/heudiconv/test.sh b/recipes/heudiconv/test.sh new file mode 100644 index 00000000..64c97d3a --- /dev/null +++ b/recipes/heudiconv/test.sh @@ -0,0 +1 @@ +heudiconv \ No newline at end of file diff --git a/recipes/template_minimal/build.sh b/recipes/template_minimal/build.sh index 71f27004..95d62b94 100644 --- a/recipes/template_minimal/build.sh +++ b/recipes/template_minimal/build.sh @@ -5,7 +5,7 @@ if [ "$1" != "" ]; then echo "Entering Debug mode" export debug=$1 fi -source ../main_setup.sh +source ../main_setup.sh --reinstall_neurodocker=false neurodocker generate ${neurodocker_buildMode} \ --base-image neurodebian:sid-non-free \