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Merge pull request #122 from miykael/spm_version_switch
Switches SPM version from dev to stable r7219
2 parents 38b9b6d + edfdaca commit 52e0c2b

9 files changed

+68
-39
lines changed

‎Dockerfile‎

Lines changed: 27 additions & 13 deletions
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@@ -1,5 +1,5 @@
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# Generated by Neurodocker version 0.4.2-dev
2-
# Timestamp: 2018-10-09 19:14:50 UTC
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# Timestamp: 2018-10-09 20:48:57 UTC
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#
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# Thank you for using Neurodocker. If you discover any issues
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# or ways to improve this software, please submit an issue or
@@ -63,9 +63,11 @@ RUN apt-get update -qq \
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RUN sed -i '$isource /etc/fsl/fsl.sh' $ND_ENTRYPOINT
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66+
ENV LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro/lib"
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ENV FORCE_SPMMCR="1" \
67-
LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/matlabmcr-2018b/v95/runtime/glnxa64:/opt/matlabmcr-2018b/v95/bin/glnxa64:/opt/matlabmcr-2018b/v95/sys/os/glnxa64:/opt/matlabmcr-2018b/v95/extern/bin/glnxa64" \
68-
MATLABCMD="/opt/matlabmcr-2018b/v95/toolbox/matlab"
69+
LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/matlabmcr-2010a/v713/runtime/glnxa64:/opt/matlabmcr-2010a/v713/bin/glnxa64:/opt/matlabmcr-2010a/v713/sys/os/glnxa64:/opt/matlabmcr-2010a/v713/extern/bin/glnxa64" \
70+
MATLABCMD="/opt/matlabmcr-2010a/v713/toolbox/matlab"
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RUN apt-get update -qq \
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&& apt-get install -y -q --no-install-recommends \
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bc \
@@ -77,19 +79,25 @@ RUN apt-get update -qq \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
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&& echo "Downloading MATLAB Compiler Runtime ..." \
80-
&& curl -fsSL --retry 5 -o /tmp/mcr.zip https://ssd.mathworks.com/supportfiles/downloads/R2018b/deployment_files/R2018b/installers/glnxa64/MCR_R2018b_glnxa64_installer.zip \
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&& unzip -q /tmp/mcr.zip -d /tmp/mcrtmp \
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&& /tmp/mcrtmp/install -destinationFolder /opt/matlabmcr-2018b -mode silent -agreeToLicense yes \
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&& curl -sSL --retry 5 -o /tmp/toinstall.deb http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb \
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&& dpkg -i /tmp/toinstall.deb \
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&& rm /tmp/toinstall.deb \
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&& apt-get install -f \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
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&& curl -fsSL --retry 5 -o /tmp/MCRInstaller.bin https://dl.dropbox.com/s/zz6me0c3v4yq5fd/MCR_R2010a_glnxa64_installer.bin \
89+
&& chmod +x /tmp/MCRInstaller.bin \
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&& /tmp/MCRInstaller.bin -silent -P installLocation="/opt/matlabmcr-2010a" \
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&& rm -rf /tmp/* \
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&& echo "Downloading standalone SPM ..." \
85-
&& curl -fsSL --retry 5 -o /tmp/spm12.zip http://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/dev/spm12_latest_Linux_R2018b.zip \
93+
&& curl -fsSL --retry 5 -o /tmp/spm12.zip http://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/previous/spm12_r7219_R2010a.zip \
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&& unzip -q /tmp/spm12.zip -d /tmp \
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&& mkdir -p /opt/spm12-dev \
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&& mv /tmp/spm12/* /opt/spm12-dev/ \
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&& chmod -R 777 /opt/spm12-dev \
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&& mkdir -p /opt/spm12-r7219 \
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&& mv /tmp/spm12/* /opt/spm12-r7219/ \
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&& chmod -R 777 /opt/spm12-r7219 \
9098
&& rm -rf /tmp/* \
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&& /opt/spm12-dev/run_spm12.sh /opt/matlabmcr-2018b/v95 quit \
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&& sed -i '$iexport SPMMCRCMD=\"/opt/spm12-dev/run_spm12.sh /opt/matlabmcr-2018b/v95 script\"' $ND_ENTRYPOINT
99+
&& /opt/spm12-r7219/run_spm12.sh /opt/matlabmcr-2010a/v713 quit \
100+
&& sed -i '$iexport SPMMCRCMD=\"/opt/spm12-r7219/run_spm12.sh /opt/matlabmcr-2010a/v713 script\"' $ND_ENTRYPOINT
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RUN useradd --no-user-group --create-home --shell /bin/bash neuro
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USER neuro
@@ -202,9 +210,15 @@ RUN echo '{ \
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\n "source /etc/fsl/fsl.sh" \
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\n ], \
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\n [ \
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\n "env", \
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\n { \
215+
\n "LD_LIBRARY_PATH": "/opt/miniconda-latest/envs/neuro/lib" \
216+
\n } \
217+
\n ], \
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\n [ \
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\n "spm12", \
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\n { \
207-
\n "version": "dev" \
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\n "version": "r7219" \
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\n } \
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\n ], \
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\n [ \

‎Singularity‎

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@@ -1,5 +1,5 @@
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# Generated by Neurodocker version 0.4.2-dev
2-
# Timestamp: 2018-10-09 19:14:51 UTC
2+
# Timestamp: 2018-10-09 20:48:58 UTC
33
#
44
# Thank you for using Neurodocker. If you discover any issues
55
# or ways to improve this software, please submit an issue or
@@ -69,19 +69,25 @@ apt-get install -y -q --no-install-recommends \
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apt-get clean
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rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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echo "Downloading MATLAB Compiler Runtime ..."
72-
curl -fsSL --retry 5 -o /tmp/mcr.zip https://ssd.mathworks.com/supportfiles/downloads/R2018b/deployment_files/R2018b/installers/glnxa64/MCR_R2018b_glnxa64_installer.zip
73-
unzip -q /tmp/mcr.zip -d /tmp/mcrtmp
74-
/tmp/mcrtmp/install -destinationFolder /opt/matlabmcr-2018b -mode silent -agreeToLicense yes
72+
curl -sSL --retry 5 -o /tmp/toinstall.deb http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb
73+
dpkg -i /tmp/toinstall.deb
74+
rm /tmp/toinstall.deb
75+
apt-get install -f
76+
apt-get clean
77+
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
78+
curl -fsSL --retry 5 -o /tmp/MCRInstaller.bin https://dl.dropbox.com/s/zz6me0c3v4yq5fd/MCR_R2010a_glnxa64_installer.bin
79+
chmod +x /tmp/MCRInstaller.bin
80+
/tmp/MCRInstaller.bin -silent -P installLocation="/opt/matlabmcr-2010a"
7581
rm -rf /tmp/*
7682
echo "Downloading standalone SPM ..."
77-
curl -fsSL --retry 5 -o /tmp/spm12.zip http://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/dev/spm12_latest_Linux_R2018b.zip
83+
curl -fsSL --retry 5 -o /tmp/spm12.zip http://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/previous/spm12_r7219_R2010a.zip
7884
unzip -q /tmp/spm12.zip -d /tmp
79-
mkdir -p /opt/spm12-dev
80-
mv /tmp/spm12/* /opt/spm12-dev/
81-
chmod -R 777 /opt/spm12-dev
85+
mkdir -p /opt/spm12-r7219
86+
mv /tmp/spm12/* /opt/spm12-r7219/
87+
chmod -R 777 /opt/spm12-r7219
8288
rm -rf /tmp/*
83-
/opt/spm12-dev/run_spm12.sh /opt/matlabmcr-2018b/v95 quit
84-
sed -i '$iexport SPMMCRCMD=\"/opt/spm12-dev/run_spm12.sh /opt/matlabmcr-2018b/v95 script\"' $ND_ENTRYPOINT
89+
/opt/spm12-r7219/run_spm12.sh /opt/matlabmcr-2010a/v713 quit
90+
sed -i '$iexport SPMMCRCMD=\"/opt/spm12-r7219/run_spm12.sh /opt/matlabmcr-2010a/v713 script\"' $ND_ENTRYPOINT
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useradd --no-user-group --create-home --shell /bin/bash neuro
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su - neuro
@@ -196,9 +202,15 @@ echo '{
196202
\n "source /etc/fsl/fsl.sh"
197203
\n ],
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\n [
205+
\n "env",
206+
\n {
207+
\n "LD_LIBRARY_PATH": "/opt/miniconda-latest/envs/neuro/lib"
208+
\n }
209+
\n ],
210+
\n [
199211
\n "spm12",
200212
\n {
201-
\n "version": "dev"
213+
\n "version": "r7219"
202214
\n }
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\n ],
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\n [
@@ -307,9 +319,10 @@ echo '{
307319
export LANG="en_US.UTF-8"
308320
export LC_ALL="en_US.UTF-8"
309321
export ND_ENTRYPOINT="/neurodocker/startup.sh"
322+
export LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro/lib"
310323
export FORCE_SPMMCR="1"
311-
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/matlabmcr-2018b/v95/runtime/glnxa64:/opt/matlabmcr-2018b/v95/bin/glnxa64:/opt/matlabmcr-2018b/v95/sys/os/glnxa64:/opt/matlabmcr-2018b/v95/extern/bin/glnxa64"
312-
export MATLABCMD="/opt/matlabmcr-2018b/v95/toolbox/matlab"
324+
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/matlabmcr-2010a/v713/runtime/glnxa64:/opt/matlabmcr-2010a/v713/bin/glnxa64:/opt/matlabmcr-2010a/v713/sys/os/glnxa64:/opt/matlabmcr-2010a/v713/extern/bin/glnxa64"
325+
export MATLABCMD="/opt/matlabmcr-2010a/v713/toolbox/matlab"
313326
export CONDA_DIR="/opt/miniconda-latest"
314327
export PATH="/opt/miniconda-latest/bin:$PATH"
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‎generate.sh‎

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@@ -11,7 +11,8 @@ generate_docker() {
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git-annex-standalone vim emacs-nox nano less ncdu \
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tig git-annex-remote-rclone octave netbase \
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--add-to-entrypoint "source /etc/fsl/fsl.sh" \
14-
--spm12 version=dev \
14+
--env LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro/lib" \
15+
--spm12 version=r7219 \
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--user=neuro \
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--miniconda miniconda_version="4.3.31" \
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conda_install="python=3.6 pytest jupyter jupyterlab jupyter_contrib_nbextensions
@@ -48,7 +49,8 @@ generate_singularity() {
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git-annex-standalone vim emacs-nox nano less ncdu \
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tig git-annex-remote-rclone octave netbase \
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--add-to-entrypoint "source /etc/fsl/fsl.sh" \
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--spm12 version=dev \
52+
--env LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro/lib" \
53+
--spm12 version=r7219 \
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--user=neuro \
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--miniconda miniconda_version="4.3.31" \
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conda_install="python=3.6 pytest jupyter jupyterlab jupyter_contrib_nbextensions

‎notebooks/advanced_spmmcr.ipynb‎

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"outputs": [],
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"source": [
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"from nipype.interfaces import spm\n",
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"matlab_cmd = '/opt/spm12-dev/run_spm12.sh /opt/matlabmcr-2018b/v95/ script'\n",
19+
"matlab_cmd = '/opt/spm12-r7219/run_spm12.sh /opt/matlabmcr-2010a/v713/ script'\n",
2020
"spm.SPMCommand.set_mlab_paths(matlab_cmd=matlab_cmd, use_mcr=True)"
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]
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},

‎notebooks/basic_error_and_crashes.ipynb‎

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"\n",
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"```python\n",
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"from nipype.interfaces.matlab import MatlabCommand\n",
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"MatlabCommand.set_default_paths('/opt/spm12-dev/spm12_mcr/spm/spm12')\n",
454+
"MatlabCommand.set_default_paths('/opt/spm12-r7219/spm12_mcr/spm12')\n",
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"```"
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]
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},

‎notebooks/basic_interfaces.ipynb‎

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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"Perfect! Exactly what we want. Hmm... what else could we want from BET? Well, it's actually a fairly complicated program. As is the case for all FSL binaries, just call it with no arguments to see all its options."
121+
"Perfect! Exactly what we want. Hmm... what else could we want from BET? Well, it's actually a fairly complicated program. As is the case for all FSL binaries, just call it with the help flag `-h` to see all its options."
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]
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},
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{

‎notebooks/example_normalize.ipynb‎

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"# Smoothing withds used during preprocessing\n",
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"fwhm = [4, 8]\n",
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"\n",
354-
"template = '/opt/spm12-dev/spm12_mcr/spm/spm12/tpm/TPM.nii'"
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"template = '/opt/spm12-r7219/spm12_mcr/spm12/tpm/TPM.nii'"
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]
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},
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{

‎notebooks/handson_analysis.ipynb‎

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"\n",
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"# Specify which SPM to use\n",
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"from nipype.interfaces.matlab import MatlabCommand\n",
53-
"MatlabCommand.set_default_paths('/opt/spm12-dev/spm12_mcr/spm/spm12')"
53+
"MatlabCommand.set_default_paths('/opt/spm12-r7219/spm12_mcr/spm12')"
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]
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},
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{
@@ -523,7 +523,7 @@
523523
"from nipype.interfaces.spm import Normalize12\n",
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"\n",
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"# Location of the template\n",
526-
"template = '/opt/spm12-dev/spm12_mcr/spm/spm12/tpm/TPM.nii'"
526+
"template = '/opt/spm12-r7219/spm12_mcr/spm12/tpm/TPM.nii'"
527527
]
528528
},
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{
@@ -973,7 +973,7 @@
973973
"outputs": [],
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"source": [
975975
"# Load GM probability map of TPM.nii\n",
976-
"img = nb.load('/opt/spm12-dev/spm12_mcr/spm/spm12/tpm/TPM.nii')\n",
976+
"img = nb.load('/opt/spm12-r7219/spm12_mcr/spm12/tpm/TPM.nii')\n",
977977
"GM_template = nb.Nifti1Image(img.get_data()[..., 0], img.affine, img.header)\n",
978978
"\n",
979979
"# Plot normalized subject anatomy\n",
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10421042
"\n",
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"# Specify which SPM to use\n",
10441044
"from nipype.interfaces.matlab import MatlabCommand\n",
1045-
"MatlabCommand.set_default_paths('/opt/spm12-dev/spm12_mcr/spm/spm12')"
1045+
"MatlabCommand.set_default_paths('/opt/spm12-r7219/spm12_mcr/spm12')"
10461046
]
10471047
},
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{
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13031303
"outputs": [],
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"source": [
13051305
"%%bash\n",
1306-
"TEMPLATE='/opt/spm12-dev/spm12_mcr/spm/spm12/tpm/TPM.nii'\n",
1306+
"TEMPLATE='/opt/spm12-r7219/spm12_mcr/spm12/tpm/TPM.nii'\n",
13071307
"\n",
13081308
"# Extract the first volume with `fslroi`\n",
13091309
"fslroi $TEMPLATE GM_PM.nii.gz 0 1\n",

‎notebooks/handson_preprocessing.ipynb‎

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"\n",
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"# Specify which SPM to use\n",
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"from nipype.interfaces.matlab import MatlabCommand\n",
81-
"MatlabCommand.set_default_paths('/opt/spm12-dev/spm12_mcr/spm/spm12')"
81+
"MatlabCommand.set_default_paths('/opt/spm12-r7219/spm12_mcr/spm12')"
8282
]
8383
},
8484
{
@@ -474,7 +474,7 @@
474474
"outputs": [],
475475
"source": [
476476
"# Use the following tissue specification to get a GM and WM probability map\n",
477-
"tpm_img ='/opt/spm12-dev/spm12_mcr/spm/spm12/tpm/TPM.nii'\n",
477+
"tpm_img ='/opt/spm12-r7219/spm12_mcr/spm12/tpm/TPM.nii'\n",
478478
"tissue1 = ((tpm_img, 1), 1, (True,False), (False, False))\n",
479479
"tissue2 = ((tpm_img, 2), 1, (True,False), (False, False))\n",
480480
"tissue3 = ((tpm_img, 3), 2, (True,False), (False, False))\n",

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