|
|
@@ -1,5 +1,5 @@
|
|
|
Bootstrap: docker
|
|
|
-From: debian:buster-slim
|
|
|
+From: debian:bookworm-slim
|
|
|
|
|
|
%setup
|
|
|
mkdir -p ${SINGULARITY_ROOTFS}/batch
|
|
|
@@ -9,64 +9,72 @@ From: debian:buster-slim
|
|
|
install -m 755 ./code/* ${SINGULARITY_ROOTFS}/code
|
|
|
|
|
|
%post
|
|
|
- apt-get update
|
|
|
- apt-get -y install wget unzip libxext6 libxt6 moreutils
|
|
|
-
|
|
|
- # download software
|
|
|
- MCRURL="https://ssd.mathworks.com/supportfiles/downloads/R2017b/deployment_files/R2017b/installers/glnxa64/MCR_R2017b_glnxa64_installer.zip"
|
|
|
- SPMURL="http://www.neuro.uni-jena.de/cat12/CAT12.7_r1743_R2017b_MCR_Linux.zip"
|
|
|
+ apt-get -qq update
|
|
|
+ apt-get --yes --quiet --no-install-recommends install \
|
|
|
+ wget \
|
|
|
+ unzip \
|
|
|
+ libxext6 \
|
|
|
+ libxt6 \
|
|
|
+ moreutils \
|
|
|
+ build-essential \
|
|
|
+ curl \
|
|
|
+ ca-certificates
|
|
|
+ DEBIAN_FRONTEND=noninteractive apt-get --yes --quiet install \
|
|
|
+ octave \
|
|
|
+ liboctave-dev
|
|
|
+
|
|
|
+ mkdir /opt/spm12
|
|
|
+ curl -fsSL --retry 5 https://github.com/spm/spm12/archive/r7771.tar.gz | tar -xzC /opt/spm12 --strip-components 1
|
|
|
+ curl -fsSL --retry 5 https://raw.githubusercontent.com/spm/spm-octave/main/spm12_r7771.patch | patch -p0
|
|
|
+ make -C /opt/spm12/src PLATFORM=octave distclean
|
|
|
+ make -C /opt/spm12/src PLATFORM=octave
|
|
|
+ make -C /opt/spm12/src PLATFORM=octave install
|
|
|
+ ln -s /opt/spm12/bin/spm12-octave /usr/local/bin/spm12
|
|
|
+
|
|
|
+ CATversion="r2560"
|
|
|
|
|
|
cd /downloads
|
|
|
- wget "${MCRURL}" && unzip -d /downloads/MCR MCR_R2017b_glnxa64_installer.zip
|
|
|
- wget "${SPMURL}" && unzip -d /code/SPM CAT12.7_r1743_R2017b_MCR_Linux.zip
|
|
|
- mv /code/SPM/CAT12.7_r1743_R2017b_MCR_Linux /code/SPM/MCR_Linux/
|
|
|
-
|
|
|
- # install MCR
|
|
|
- /downloads/MCR/install -mode silent -agreeToLicense yes
|
|
|
-
|
|
|
- # install SPM
|
|
|
- /code/SPM/MCR_Linux/run_spm12.sh /usr/local/MATLAB/MATLAB_Runtime/v93 quit
|
|
|
- cd /code/SPM/MCR_Linux && chmod +rx run_spm12.sh spm12.sh spm12
|
|
|
+ wget http://www.neuro.uni-jena.de/cat12/cat12_${CATversion}.zip && unzip -d /opt/spm12/toolbox/ cat12_${CATversion}.zip
|
|
|
+ rm -fr /downloads
|
|
|
|
|
|
# install CAT standalone interface
|
|
|
- STANDALONE="/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/standalone"
|
|
|
+ STANDALONE="/opt/spm12/toolbox/cat12/standalone"
|
|
|
cd ${STANDALONE} && chmod +rx *.sh
|
|
|
cd /code && ln -s ${STANDALONE}/*.sh .
|
|
|
- cd /batch && ln -s ${STANDALONE}/*.txt .
|
|
|
+ cd /batch && ln -s ${STANDALONE}/*.m .
|
|
|
|
|
|
# set permissions
|
|
|
find /code -type f -print0 | xargs -0 chmod +r
|
|
|
- find /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/CAT.glnx86 -type f -print0 | xargs -0 chmod +rx
|
|
|
|
|
|
- rm -fr /downloads
|
|
|
-
|
|
|
- apt-get clean
|
|
|
- apt-get autoremove
|
|
|
+ rm -f /opt/spm12/src/*.{mex,o,a}
|
|
|
+ apt-get --yes remove build-essential curl liboctave-dev
|
|
|
+ apt-get --yes autoremove
|
|
|
+ apt-get --yes clean
|
|
|
|
|
|
%environment
|
|
|
- export SPMROOT=/code/SPM/MCR_Linux
|
|
|
- export MCRROOT=/usr/local/MATLAB/MATLAB_Runtime/v93
|
|
|
- export MCR_INHIBIT_CTF_LOCK=1
|
|
|
+ export SPM_HOME=/opt/spm12
|
|
|
|
|
|
%runscript
|
|
|
- exec /code/main "$@"
|
|
|
+ exec /code/main "$@"
|
|
|
|
|
|
%labels
|
|
|
- Author Malgorzata Wierzba (m.wierzba@fz-juelich.de)
|
|
|
- Version 1.0.1
|
|
|
+ Author fil.spm@ucl.ac.uk
|
|
|
+ Malgorzata Wierzba (m.wierzba@fz-juelich.de)
|
|
|
+ Felix Hoffstaedter (f.hoffstaedter@fz-juelich.de)
|
|
|
+ Version v1.1
|
|
|
|
|
|
%help
|
|
|
+ This is a container with SPM12, CAT12 and GNU Octave.
|
|
|
|
|
|
-This container allows to run the standalone, compiled version of the
|
|
|
+This container allows to run the standalone version of the
|
|
|
Computational Anatomy Toolbox (CAT), which is an extension to SPM
|
|
|
-software. Using the container does not require the availability of a
|
|
|
-MATLAB licence.
|
|
|
+software using Octave 7.3.0
|
|
|
|
|
|
-The container includes:
|
|
|
+The container runs Debian bookworm-slim and includes:
|
|
|
|
|
|
-- MATLAB Compiler Runtime (R2017b, 9.3)
|
|
|
+- Octave (7.3.0)
|
|
|
- Standalone version of SPM software (SPM12, r7771)
|
|
|
-- Computational Anatomy Toolbox (CAT12.7 r1743)
|
|
|
+- Computational Anatomy Toolbox (CAT12.9 ${CATversion})
|
|
|
- CAT interface scripts (cat_standalone.sh, cat_parallelize.sh).
|
|
|
|
|
|
For more details on the exact version of the software used in this
|
|
|
@@ -79,8 +87,8 @@ In principle this container allows you to perform the very same types
|
|
|
of analysis that are possible with the standalone version of CAT. It
|
|
|
is assumed that the user is familiar with the content of the batch
|
|
|
files dedicated for the use with the standalone version of CAT
|
|
|
-(cat_standalone_segment.txt, cat_standalone_simple.txt,
|
|
|
-cat_standalone_resample.txt, cat_standalone_smooth.txt) and can modify
|
|
|
+(cat_standalone_segment.m, cat_standalone_simple.m,
|
|
|
+cat_standalone_resample.m, cat_standalone_smooth.m) and can modify
|
|
|
their content according to his/her needs. For more details, please
|
|
|
refer to the CAT12 documentation and manual.
|
|
|
|
|
|
@@ -94,12 +102,12 @@ singularity run <container> <subcommand> <batch file> <arguments>
|
|
|
|
|
|
To view a batch file, use the 'view' subcommand:
|
|
|
|
|
|
-singularity run container.simg view cat_standalone_smooth.txt
|
|
|
+singularity run container.simg view cat_standalone_smooth.m
|
|
|
|
|
|
To copy a batch file to your computer, use the 'copy' subcommand and
|
|
|
specify destination path as an additional argument:
|
|
|
|
|
|
-singularity run container.simg copy cat_standalone_smooth.txt $HOME
|
|
|
+singularity run container.simg copy cat_standalone_smooth.m $HOME
|
|
|
|
|
|
Make sure that the specified path is mounted to the container (more
|
|
|
information on this can be found below) and that you have write access
|
|
|
@@ -118,12 +126,12 @@ singularity run --cleanenv <container> <batch file> <arguments>
|
|
|
To use a default batch file, use one of the files included in the
|
|
|
container ('/batch'):
|
|
|
singularity run --cleanenv container.simg \
|
|
|
- -b /batch/cat_standalone_segment.txt \
|
|
|
+ -b /batch/cat_standalone_segment.m \
|
|
|
T1.nii
|
|
|
|
|
|
To use your own, customised batch file, simply specify its path:
|
|
|
singularity run --cleanenv container.simg \
|
|
|
- -b $HOME/cat_standalone_segment.txt \
|
|
|
+ -b $HOME/cat_standalone_segment.m \
|
|
|
T1.nii
|
|
|
|
|
|
|
|
|
@@ -140,7 +148,7 @@ of the '/data' folder on your computer available in the '/mnt' folder
|
|
|
inside the container, specify the mount point in the following way:
|
|
|
|
|
|
singularity run --cleanenv --bind /data:/mnt container.simg \
|
|
|
- -b /batch/cat_standalone_segment.txt \
|
|
|
+ -b /batch/cat_standalone_segment.m \
|
|
|
/mnt/T1.nii
|
|
|
|
|
|
|
|
|
@@ -148,39 +156,33 @@ EXAMPLES:
|
|
|
|
|
|
CAT12 segmentation batch:
|
|
|
singularity run --cleanenv container.simg \
|
|
|
- -b cat_standalone_segment.txt \
|
|
|
+ -b cat_standalone_segment.m \
|
|
|
T1.nii
|
|
|
|
|
|
CAT12 simple processing batch:
|
|
|
singularity run --cleanenv container.simg \
|
|
|
- -b cat_standalone_simple.txt \
|
|
|
+ -b cat_standalone_simple.m \
|
|
|
T1.nii
|
|
|
|
|
|
CAT12 resample & smooth batch:
|
|
|
singularity run --cleanenv container.simg \
|
|
|
- -b cat_standalone_resample.txt \
|
|
|
+ -b cat_standalone_resample.m \
|
|
|
-a1 "12" -a2 "1" \
|
|
|
lh.thickness.T1
|
|
|
|
|
|
CAT12 volume smoothing batch:
|
|
|
singularity run --cleanenv container.simg \
|
|
|
- -b cat_standalone_smooth.txt \
|
|
|
+ -b cat_standalone_smooth.m \
|
|
|
-a1 "[6 6 6]" -a2 "'s6'" \
|
|
|
T1.nii
|
|
|
|
|
|
|
|
|
-Known issues:
|
|
|
-
|
|
|
-- Parallelization with cat_parallelize.sh is not implemented yet.
|
|
|
-- Longitudinal segmentation with cat_standalone_segment_long.txt
|
|
|
- is not tested yet.
|
|
|
-
|
|
|
|
|
|
Contact information:
|
|
|
|
|
|
Any problems or concerns regarding this container should be reported
|
|
|
-to Malgorzata Wierzba (m.wierzba@fz-juelich.de) or Michael Hanke
|
|
|
-(m.hanke@fz-juelich.de).
|
|
|
+to Felix Hoffstaedter (f.hoffstaedter@fz-juelich.de) and regarding
|
|
|
+CAT12 to Christian Gaser (christian.gaser@uni-jena.de)
|
|
|
|
|
|
|
|
|
Acknowledgements:
|
|
|
@@ -194,9 +196,7 @@ Licence.
|
|
|
The SPM software (https://www.fil.ion.ucl.ac.uk/spm/) is developed by
|
|
|
the Wellcome Trust Centre for Neuroimaging and is free but copyright
|
|
|
software, distributed under the terms of the GNU General Public
|
|
|
-Licence.
|
|
|
+Licence (GPL).
|
|
|
|
|
|
-MATLAB Compiler Runtime
|
|
|
-(https://uk.mathworks.com/products/compiler/matlab-runtime.html) is
|
|
|
-developed by the The MathWorks, Inc. and is subject to the MATLAB
|
|
|
-Runtime licence.
|
|
|
+GNU Octave is a freely redistributable software under the terms of
|
|
|
+the GPL as published by the Free Software Foundation.
|
