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miykaelmiykael
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ENH: switch SPM to stable version
1 parent acd082c commit 2497497

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-38
lines changed

‎Dockerfile‎

Lines changed: 13 additions & 13 deletions
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@@ -1,5 +1,5 @@
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# Generated by Neurodocker version 0.4.2-dev
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# Timestamp: 2018-10-04 07:38:10 UTC
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# Timestamp: 2018-10-04 11:47:31 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
@@ -64,8 +64,8 @@ RUN apt-get update -qq \
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RUN sed -i '$isource /etc/fsl/fsl.sh' $ND_ENTRYPOINT
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ENV FORCE_SPMMCR="1" \
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LD_LIBRARY_PATH="$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"
67+
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" \
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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 \
@@ -76,19 +76,19 @@ 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 ..." \
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&& 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 -fsSL --retry 5 -o /tmp/MCRInstaller.bin https://dl.dropbox.com/s/zz6me0c3v4yq5fd/MCR_R2010a_glnxa64_installer.bin \
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&& 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 ..." \
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&& 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 \
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&& 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 \
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&& 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\"' $ND_ENTRYPOINT
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&& /opt/spm12-r7219/run_spm12.sh /opt/matlabmcr-2010a/v713 quit \
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&& sed -i '$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
@@ -203,7 +203,7 @@ RUN echo '{ \
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\n [ \
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\n "spm12", \
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\n { \
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\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: 2018-10-04 07:38:11 UTC
2+
# Timestamp: 2018-10-04 11:47:32 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
@@ -68,19 +68,19 @@ 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 ..."
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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
72-
unzip -q /tmp/mcr.zip -d /tmp/mcrtmp
73-
/tmp/mcrtmp/install -destinationFolder /opt/matlabmcr-2018b -mode silent -agreeToLicense yes
71+
curl -fsSL --retry 5 -o /tmp/MCRInstaller.bin https://dl.dropbox.com/s/zz6me0c3v4yq5fd/MCR_R2010a_glnxa64_installer.bin
72+
chmod +x /tmp/MCRInstaller.bin
73+
/tmp/MCRInstaller.bin -silent -P installLocation="/opt/matlabmcr-2010a"
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rm -rf /tmp/*
7575
echo "Downloading standalone SPM ..."
76-
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
76+
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
78-
mkdir -p /opt/spm12-dev
79-
mv /tmp/spm12/* /opt/spm12-dev/
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chmod -R 777 /opt/spm12-dev
78+
mkdir -p /opt/spm12-r7219
79+
mv /tmp/spm12/* /opt/spm12-r7219/
80+
chmod -R 777 /opt/spm12-r7219
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rm -rf /tmp/*
82-
/opt/spm12-dev/run_spm12.sh /opt/matlabmcr-2018b/v95 quit
83-
sed -i '$iexport SPMMCRCMD=\"/opt/spm12-dev/run_spm12.sh /opt/matlabmcr-2018b/v95 script\"' $ND_ENTRYPOINT
82+
/opt/spm12-r7219/run_spm12.sh /opt/matlabmcr-2010a/v713 quit
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sed -i '$iexport SPMMCRCMD=\"/opt/spm12-r7219/run_spm12.sh /opt/matlabmcr-2010a/v713 script\"' $ND_ENTRYPOINT
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useradd --no-user-group --create-home --shell /bin/bash neuro
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su - neuro
@@ -197,7 +197,7 @@ echo '{
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\n [
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\n "spm12",
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\n {
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\n "version": "dev"
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\n "version": "r7219"
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\n }
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\n ],
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\n [
@@ -307,8 +307,8 @@ export LANG="en_US.UTF-8"
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export LC_ALL="en_US.UTF-8"
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export ND_ENTRYPOINT="/neurodocker/startup.sh"
309309
export FORCE_SPMMCR="1"
310-
export LD_LIBRARY_PATH="$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"
311-
export MATLABCMD="/opt/matlabmcr-2018b/v95/toolbox/matlab"
310+
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/matlabmcr-2010a/v713/runtime/glnxa64:/opt/matlabmcr-2010a/v713/bin/glnxa64:/opt/matlabmcr-2010a/v713/sys/os/glnxa64:/opt/matlabmcr-2010a/v713/extern/bin/glnxa64"
311+
export MATLABCMD="/opt/matlabmcr-2010a/v713/toolbox/matlab"
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export CONDA_DIR="/opt/miniconda-latest"
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export PATH="/opt/miniconda-latest/bin:$PATH"
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‎generate.sh‎

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@@ -11,7 +11,7 @@ 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" \
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--spm12 version=dev \
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--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 +48,7 @@ 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 \
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--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",
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"matlab_cmd = '/opt/spm12-r7219/run_spm12.sh /opt/matlabmcr-2018b/v95/ script'\n",
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"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",
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"MatlabCommand.set_default_paths('/opt/spm12-r7219/spm12_mcr/spm/spm12')\n",
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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",
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"template = '/opt/spm12-dev/spm12_mcr/spm/spm12/tpm/TPM.nii'"
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"template = '/opt/spm12-r7219/spm12_mcr/spm/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')"
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"MatlabCommand.set_default_paths('/opt/spm12-r7219/spm12_mcr/spm/spm12')"
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]
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},
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{
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"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'"
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"template = '/opt/spm12-r7219/spm12_mcr/spm/spm12/tpm/TPM.nii'"
527527
]
528528
},
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{
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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/spm/spm12/tpm/TPM.nii')\n",
977977
"GM_template = nb.Nifti1Image(img.get_data()[..., 0], img.affine, img.header)\n",
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"\n",
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"# Plot normalized subject anatomy\n",
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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",
1045-
"MatlabCommand.set_default_paths('/opt/spm12-dev/spm12_mcr/spm/spm12')"
1045+
"MatlabCommand.set_default_paths('/opt/spm12-r7219/spm12_mcr/spm/spm12')"
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]
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},
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{
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13031303
"outputs": [],
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"source": [
13051305
"%%bash\n",
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"TEMPLATE='/opt/spm12-dev/spm12_mcr/spm/spm12/tpm/TPM.nii'\n",
1306+
"TEMPLATE='/opt/spm12-r7219/spm12_mcr/spm/spm12/tpm/TPM.nii'\n",
13071307
"\n",
13081308
"# Extract the first volume with `fslroi`\n",
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"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/spm/spm12')"
8282
]
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},
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{
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474474
"outputs": [],
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"source": [
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"# 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/spm/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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