Skip to content

Commit 52e0c2b

Browse files
miykaelmiykael
authored
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
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
# Generated by Neurodocker version 0.4.2-dev
2-
# Timestamp: 2018-10-09 19:14:50 UTC
2+
# Timestamp: 2018-10-09 20:48:57 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
@@ -63,9 +63,11 @@ RUN apt-get update -qq \
6363

6464
RUN sed -i '$isource /etc/fsl/fsl.sh' $ND_ENTRYPOINT
6565

66+
ENV LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro/lib"
67+
6668
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"
6971
RUN apt-get update -qq \
7072
&& apt-get install -y -q --no-install-recommends \
7173
bc \
@@ -77,19 +79,25 @@ RUN apt-get update -qq \
7779
&& apt-get clean \
7880
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
7981
&& 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 \
81-
&& unzip -q /tmp/mcr.zip -d /tmp/mcrtmp \
82-
&& /tmp/mcrtmp/install -destinationFolder /opt/matlabmcr-2018b -mode silent -agreeToLicense yes \
82+
&& curl -sSL --retry 5 -o /tmp/toinstall.deb http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb \
83+
&& dpkg -i /tmp/toinstall.deb \
84+
&& rm /tmp/toinstall.deb \
85+
&& apt-get install -f \
86+
&& apt-get clean \
87+
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
88+
&& 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 \
90+
&& /tmp/MCRInstaller.bin -silent -P installLocation="/opt/matlabmcr-2010a" \
8391
&& rm -rf /tmp/* \
8492
&& 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 \
8694
&& unzip -q /tmp/spm12.zip -d /tmp \
87-
&& mkdir -p /opt/spm12-dev \
88-
&& mv /tmp/spm12/* /opt/spm12-dev/ \
89-
&& chmod -R 777 /opt/spm12-dev \
95+
&& mkdir -p /opt/spm12-r7219 \
96+
&& mv /tmp/spm12/* /opt/spm12-r7219/ \
97+
&& chmod -R 777 /opt/spm12-r7219 \
9098
&& rm -rf /tmp/* \
91-
&& /opt/spm12-dev/run_spm12.sh /opt/matlabmcr-2018b/v95 quit \
92-
&& 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
93101

94102
RUN useradd --no-user-group --create-home --shell /bin/bash neuro
95103
USER neuro
@@ -202,9 +210,15 @@ RUN echo '{ \
202210
\n "source /etc/fsl/fsl.sh" \
203211
\n ], \
204212
\n [ \
213+
\n "env", \
214+
\n { \
215+
\n "LD_LIBRARY_PATH": "/opt/miniconda-latest/envs/neuro/lib" \
216+
\n } \
217+
\n ], \
218+
\n [ \
205219
\n "spm12", \
206220
\n { \
207-
\n "version": "dev" \
221+
\n "version": "r7219" \
208222
\n } \
209223
\n ], \
210224
\n [ \

‎Singularity

Lines changed: 26 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
# 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 \
6969
apt-get clean
7070
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
7171
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
8591

8692
useradd --no-user-group --create-home --shell /bin/bash neuro
8793
su - neuro
@@ -196,9 +202,15 @@ echo '{
196202
\n "source /etc/fsl/fsl.sh"
197203
\n ],
198204
\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 }
203215
\n ],
204216
\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"
315328

‎generate.sh

Lines changed: 4 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -11,7 +11,8 @@ generate_docker() {
1111
git-annex-standalone vim emacs-nox nano less ncdu \
1212
tig git-annex-remote-rclone octave netbase \
1313
--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 \
1516
--user=neuro \
1617
--miniconda miniconda_version="4.3.31" \
1718
conda_install="python=3.6 pytest jupyter jupyterlab jupyter_contrib_nbextensions
@@ -48,7 +49,8 @@ generate_singularity() {
4849
git-annex-standalone vim emacs-nox nano less ncdu \
4950
tig git-annex-remote-rclone octave netbase \
5051
--add-to-entrypoint "source /etc/fsl/fsl.sh" \
51-
--spm12 version=dev \
52+
--env LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro/lib" \
53+
--spm12 version=r7219 \
5254
--user=neuro \
5355
--miniconda miniconda_version="4.3.31" \
5456
conda_install="python=3.6 pytest jupyter jupyterlab jupyter_contrib_nbextensions

‎notebooks/advanced_spmmcr.ipynb

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -16,7 +16,7 @@
1616
"outputs": [],
1717
"source": [
1818
"from nipype.interfaces import spm\n",
19-
"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)"
2121
]
2222
},

‎notebooks/basic_error_and_crashes.ipynb

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -451,7 +451,7 @@
451451
"\n",
452452
"```python\n",
453453
"from nipype.interfaces.matlab import MatlabCommand\n",
454-
"MatlabCommand.set_default_paths('/opt/spm12-dev/spm12_mcr/spm/spm12')\n",
454+
"MatlabCommand.set_default_paths('/opt/spm12-r7219/spm12_mcr/spm12')\n",
455455
"```"
456456
]
457457
},

‎notebooks/basic_interfaces.ipynb

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -118,7 +118,7 @@
118118
"cell_type": "markdown",
119119
"metadata": {},
120120
"source": [
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 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."
122122
]
123123
},
124124
{

‎notebooks/example_normalize.ipynb

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -351,7 +351,7 @@
351351
"# Smoothing withds used during preprocessing\n",
352352
"fwhm = [4, 8]\n",
353353
"\n",
354-
"template = '/opt/spm12-dev/spm12_mcr/spm/spm12/tpm/TPM.nii'"
354+
"template = '/opt/spm12-r7219/spm12_mcr/spm12/tpm/TPM.nii'"
355355
]
356356
},
357357
{

‎notebooks/handson_analysis.ipynb

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -50,7 +50,7 @@
5050
"\n",
5151
"# Specify which SPM to use\n",
5252
"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')"
5454
]
5555
},
5656
{
@@ -523,7 +523,7 @@
523523
"from nipype.interfaces.spm import Normalize12\n",
524524
"\n",
525525
"# 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
},
529529
{
@@ -973,7 +973,7 @@
973973
"outputs": [],
974974
"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",
@@ -1042,7 +1042,7 @@
10421042
"\n",
10431043
"# 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
},
10481048
{
@@ -1303,7 +1303,7 @@
13031303
"outputs": [],
13041304
"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

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -78,7 +78,7 @@
7878
"\n",
7979
"# Specify which SPM to use\n",
8080
"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",

0 commit comments

Comments
 (0)