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@@ -14,11 +14,12 @@ From: debian:buster-slim
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# download software
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# download software
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MCRURL="https://ssd.mathworks.com/supportfiles/downloads/R2017b/deployment_files/R2017b/installers/glnxa64/MCR_R2017b_glnxa64_installer.zip"
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MCRURL="https://ssd.mathworks.com/supportfiles/downloads/R2017b/deployment_files/R2017b/installers/glnxa64/MCR_R2017b_glnxa64_installer.zip"
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- SPMURL="http://www.neuro.uni-jena.de/cat12/cat12_latest_R2017b_MCR_Linux.zip"
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+ SPMURL="http://www.neuro.uni-jena.de/cat12/CAT12.7_r1743_R2017b_MCR_Linux.zip"
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cd /downloads
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cd /downloads
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wget "${MCRURL}" && unzip -d /downloads/MCR MCR_R2017b_glnxa64_installer.zip
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wget "${MCRURL}" && unzip -d /downloads/MCR MCR_R2017b_glnxa64_installer.zip
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- wget "${SPMURL}" && unzip -d /code/SPM cat12_latest_R2017b_MCR_Linux.zip
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+ wget "${SPMURL}" && unzip -d /code/SPM CAT12.7_r1743_R2017b_MCR_Linux.zip
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+ mv /code/SPM/CAT12.7_r1743_R2017b_MCR_Linux /code/SPM/MCR_Linux/
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# install MCR
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# install MCR
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/downloads/MCR/install -mode silent -agreeToLicense yes
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/downloads/MCR/install -mode silent -agreeToLicense yes
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@@ -36,7 +37,7 @@ From: debian:buster-slim
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# set permissions
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# set permissions
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find /code -type f -print0 | xargs -0 chmod +r
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find /code -type f -print0 | xargs -0 chmod +r
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find /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/CAT.glnx86 -type f -print0 | xargs -0 chmod +rx
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find /code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/CAT.glnx86 -type f -print0 | xargs -0 chmod +rx
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-
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+
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rm -fr /downloads
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rm -fr /downloads
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apt-get clean
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apt-get clean
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@@ -63,9 +64,9 @@ MATLAB licence.
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The container includes:
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The container includes:
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-- MATLAB Compiler Runtime (R2017b, 9.3)
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-- Standalone version of SPM software (SPM12, r7771)
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-- Computational Anatomy Toolbox (CAT12.7-RC2 r1720)
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+- MATLAB Compiler Runtime (R2017b, 9.3)
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+- Standalone version of SPM software (SPM12, r7771)
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+- Computational Anatomy Toolbox (CAT12.7 r1743)
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- CAT interface scripts (cat_standalone.sh, cat_parallelize.sh).
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- CAT interface scripts (cat_standalone.sh, cat_parallelize.sh).
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For more details on the exact version of the software used in this
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For more details on the exact version of the software used in this
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@@ -111,11 +112,11 @@ singularity run container.simg copy all $HOME
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-- Running CAT --
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-- Running CAT --
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-Run the CAT analysis with the following command:
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+Run the CAT analysis with the following command:
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singularity run --cleanenv <container> <batch file> <arguments>
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singularity run --cleanenv <container> <batch file> <arguments>
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To use a default batch file, use one of the files included in the
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To use a default batch file, use one of the files included in the
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-container ('/batch'):
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+container ('/batch'):
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singularity run --cleanenv container.simg \
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singularity run --cleanenv container.simg \
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-b /batch/cat_standalone_segment.txt \
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-b /batch/cat_standalone_segment.txt \
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T1.nii
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T1.nii
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@@ -145,23 +146,23 @@ singularity run --cleanenv --bind /data:/mnt container.simg \
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EXAMPLES:
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EXAMPLES:
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-CAT12 segmentation batch:
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+CAT12 segmentation batch:
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singularity run --cleanenv container.simg \
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singularity run --cleanenv container.simg \
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-b cat_standalone_segment.txt \
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-b cat_standalone_segment.txt \
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T1.nii
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T1.nii
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-CAT12 simple processing batch:
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+CAT12 simple processing batch:
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singularity run --cleanenv container.simg \
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singularity run --cleanenv container.simg \
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-b cat_standalone_simple.txt \
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-b cat_standalone_simple.txt \
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T1.nii
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T1.nii
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-CAT12 resample & smooth batch:
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+CAT12 resample & smooth batch:
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singularity run --cleanenv container.simg \
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singularity run --cleanenv container.simg \
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-b cat_standalone_resample.txt \
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-b cat_standalone_resample.txt \
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-a1 "12" -a2 "1" \
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-a1 "12" -a2 "1" \
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lh.thickness.T1
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lh.thickness.T1
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-CAT12 volume smoothing batch:
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+CAT12 volume smoothing batch:
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singularity run --cleanenv container.simg \
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singularity run --cleanenv container.simg \
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-b cat_standalone_smooth.txt \
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-b cat_standalone_smooth.txt \
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-a1 "[6 6 6]" -a2 "'s6'" \
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-a1 "[6 6 6]" -a2 "'s6'" \
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@@ -171,7 +172,7 @@ singularity run --cleanenv container.simg \
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Known issues:
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Known issues:
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- Parallelization with cat_parallelize.sh is not implemented yet.
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- Parallelization with cat_parallelize.sh is not implemented yet.
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-- Longitudinal segmentation with cat_standalone_segment_long.txt
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+- Longitudinal segmentation with cat_standalone_segment_long.txt
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is not tested yet.
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is not tested yet.
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