@@ -15,65 +15,81 @@ RUN apt-get update && \
1515 build-essential \
1616 autoconf \
1717 libtool \
18- pkg-config && \
19- curl -sSL http://neuro.debian.net/lists/xenial.us-ca.full >> /etc/apt/sources.list.d/neurodebian.sources.list && \
20- apt-key add /root/.neurodebian.gpg && \
21- (apt-key adv --refresh-keys --keyserver hkp://ha.pool.sks-keyservers.net 0xA5D32F012649A5A9 || true) && \
22- apt-get update
18+ pkg-config \
19+ git && \
20+ curl -sL https://deb.nodesource.com/setup_10.x | bash - && \
21+ apt-get install -y --no-install-recommends \
22+ nodejs && \
23+ apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
24+
25+ # Install latest pandoc
26+ RUN curl -o pandoc-2.2.2.1-1-amd64.deb -sSL "https://github.com/jgm/pandoc/releases/download/2.2.2.1/pandoc-2.2.2.1-1-amd64.deb" && \
27+ dpkg -i pandoc-2.2.2.1-1-amd64.deb && \
28+ rm pandoc-2.2.2.1-1-amd64.deb
2329
2430# Installing freesurfer
2531RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1.tar.gz | tar zxv --no-same-owner -C /opt \
26- --exclude='freesurfer/trctrain' \
32+ --exclude='freesurfer/diffusion' \
33+ --exclude='freesurfer/docs' \
34+ --exclude='freesurfer/fsfast' \
35+ --exclude='freesurfer/lib/cuda' \
36+ --exclude='freesurfer/lib/qt' \
37+ --exclude='freesurfer/matlab' \
38+ --exclude='freesurfer/mni/share/man' \
2739 --exclude='freesurfer/subjects/fsaverage_sym' \
2840 --exclude='freesurfer/subjects/fsaverage3' \
2941 --exclude='freesurfer/subjects/fsaverage4' \
3042 --exclude='freesurfer/subjects/cvs_avg35' \
3143 --exclude='freesurfer/subjects/cvs_avg35_inMNI152' \
3244 --exclude='freesurfer/subjects/bert' \
45+ --exclude='freesurfer/subjects/lh.EC_average' \
46+ --exclude='freesurfer/subjects/rh.EC_average' \
47+ --exclude='freesurfer/subjects/sample-*.mgz' \
3348 --exclude='freesurfer/subjects/V1_average' \
34- --exclude='freesurfer/average/mult-comp-cor' \
35- --exclude='freesurfer/lib/cuda' \
36- --exclude='freesurfer/lib/qt'
49+ --exclude='freesurfer/trctrain'
3750
38- ENV FSL_DIR=/usr/share/fsl/5.0 \
39- OS=Linux \
51+ ENV FSL_DIR=" /usr/share/fsl/5.0"
52+ OS=" Linux"
4053 FS_OVERRIDE=0 \
41- FIX_VERTEX_AREA= \
42- FSF_OUTPUT_FORMAT=nii.gz \
43- FREESURFER_HOME=/opt/freesurfer
44- ENV SUBJECTS_DIR=$FREESURFER_HOME/subjects \
45- FUNCTIONALS_DIR=$FREESURFER_HOME/sessions \
46- MNI_DIR=$FREESURFER_HOME/mni \
47- LOCAL_DIR=$FREESURFER_HOME/local \
48- FSFAST_HOME=$FREESURFER_HOME/fsfast \
49- MINC_BIN_DIR=$FREESURFER_HOME/mni/bin \
50- MINC_LIB_DIR=$FREESURFER_HOME/mni/lib \
51- MNI_DATAPATH=$FREESURFER_HOME/mni/data \
52- FMRI_ANALYSIS_DIR=$FREESURFER_HOME/fsfast
53- ENV PERL5LIB=$MINC_LIB_DIR/perl5/5.8.5 \
54- MNI_PERL5LIB=$MINC_LIB_DIR/perl5/5.8.5 \
55- PATH=$FREESURFER_HOME/bin:$FSFAST_HOME/bin:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH
54+ FIX_VERTEX_AREA="" \
55+ FSF_OUTPUT_FORMAT="nii.gz" \
56+ FREESURFER_HOME="/opt/freesurfer"
57+ ENV SUBJECTS_DIR="$FREESURFER_HOME/subjects" \
58+ FUNCTIONALS_DIR="$FREESURFER_HOME/sessions" \
59+ MNI_DIR="$FREESURFER_HOME/mni" \
60+ LOCAL_DIR="$FREESURFER_HOME/local" \
61+ MINC_BIN_DIR="$FREESURFER_HOME/mni/bin" \
62+ MINC_LIB_DIR="$FREESURFER_HOME/mni/lib" \
63+ MNI_DATAPATH="$FREESURFER_HOME/mni/data"
64+ ENV PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
65+ MNI_PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
66+ PATH="$FREESURFER_HOME/bin:$FSFAST_HOME/bin:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH"
5667
5768# Installing Neurodebian packages (FSL, AFNI, git)
69+ RUN curl -sSL "http://neuro.debian.net/lists/$( lsb_release -c | cut -f2 ).us-ca.full" >> /etc/apt/sources.list.d/neurodebian.sources.list && \
70+ apt-key add /root/.neurodebian.gpg && \
71+ (apt-key adv --refresh-keys --keyserver hkp://ha.pool.sks-keyservers.net 0xA5D32F012649A5A9 || true)
72+
5873RUN apt-get update && \
5974 apt-get install -y --no-install-recommends \
6075 fsl-core=5.0.9-5~nd16.04+1 \
61- fsl-mni152-templates=5.0.7-2 \
6276 afni=16.2.07~dfsg.1-5~nd16.04+1 \
63- convert3d
64-
65- ENV FSLDIR=/usr/share/fsl/5.0 \
66- FSLOUTPUTTYPE=NIFTI_GZ \
67- FSLMULTIFILEQUIT=TRUE \
68- POSSUMDIR=/usr/share/fsl/5.0 \
69- LD_LIBRARY_PATH=/usr/lib/fsl/5.0:$LD_LIBRARY_PATH \
70- FSLTCLSH=/usr/bin/tclsh \
71- FSLWISH=/usr/bin/wish \
72- AFNI_MODELPATH=/usr/lib/afni/models \
73- AFNI_IMSAVE_WARNINGS=NO \
74- AFNI_TTATLAS_DATASET=/usr/share/afni/atlases \
75- AFNI_PLUGINPATH=/usr/lib/afni/plugins
76- ENV PATH=/usr/lib/fsl/5.0:/usr/lib/afni/bin:$PATH
77+ convert3d \
78+ git-annex-standalone && \
79+ apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
80+
81+ ENV FSLDIR="/usr/share/fsl/5.0" \
82+ FSLOUTPUTTYPE="NIFTI_GZ" \
83+ FSLMULTIFILEQUIT="TRUE" \
84+ POSSUMDIR="/usr/share/fsl/5.0" \
85+ LD_LIBRARY_PATH="/usr/lib/fsl/5.0:$LD_LIBRARY_PATH" \
86+ FSLTCLSH="/usr/bin/tclsh" \
87+ FSLWISH="/usr/bin/wish" \
88+ AFNI_MODELPATH="/usr/lib/afni/models" \
89+ AFNI_IMSAVE_WARNINGS="NO" \
90+ AFNI_TTATLAS_DATASET="/usr/share/afni/atlases" \
91+ AFNI_PLUGINPATH="/usr/lib/afni/plugins"
92+ ENV PATH="/usr/lib/fsl/5.0:/usr/lib/afni/bin:$PATH"
7793
7894# Installing ANTs 2.2.0 (NeuroDocker build)
7995ENV ANTSPATH=/usr/lib/ants
@@ -123,8 +139,7 @@ RUN conda install -y python=3.7.1 \
123139 libxslt=1.1.32 \
124140 graphviz=2.40.1 \
125141 traits=4.6.0 \
126- # Make sure zlib is installed
127- zlib; sync && \
142+ zlib; sync && \
128143 chmod -R a+rX /usr/local/miniconda; sync && \
129144 chmod +x /usr/local/miniconda/bin/*; sync && \
130145 conda clean --all -y; sync && \
@@ -134,49 +149,47 @@ RUN conda install -y python=3.7.1 \
134149RUN python -c "from matplotlib import font_manager" && \
135150 sed -i 's/\( backend *: \) .*$/\1 Agg/g' $( python -c "import matplotlib; print(matplotlib.matplotlib_fname())" )
136151
137- # Installing Ubuntu packages and cleaning up
138- RUN apt-get update && \
139- apt-get install -y --no-install-recommends \
140- git=1:2.7.4-0ubuntu1 && \
141- apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
142-
143- # Install latest pandoc
144- RUN curl -o pandoc-2.2.2.1-1-amd64.deb -sSL "https://github.com/jgm/pandoc/releases/download/2.2.2.1/pandoc-2.2.2.1-1-amd64.deb" && \
145- dpkg -i pandoc-2.2.2.1-1-amd64.deb && \
146- rm pandoc-2.2.2.1-1-amd64.deb
147-
148152# Unless otherwise specified each process should only use one thread - nipype
149153# will handle parallelization
150154ENV MKL_NUM_THREADS=1 \
151155 OMP_NUM_THREADS=1
152156
153- WORKDIR /root/
154-
155157# Precaching atlases
156- ENV CRN_SHARED_DATA /templateflow
157- ADD docker/scripts/get_templates.sh get_templates.sh
158- RUN mkdir $CRN_SHARED_DATA && \
159- /root/get_templates.sh && \
160- find $CRN_SHARED_DATA -type d -exec chmod 555 {} \; && \
161- find $CRN_SHARED_DATA -type f -exec chmod 444 {} \; && \
162- chmod +w $CRN_SHARED_DATA
158+ WORKDIR /opt
159+ ENV TEMPLATEFLOW_HOME="/opt/templateflow"
160+ RUN pip install "datalad==0.10.0" && \
161+ rm -rf ~/.cache/pip
162+
163+ RUN git config --global user.name "First Last" && \
164+ git config --global user.email
"[email protected] " && \
165+ datalad install -r https://github.com/templateflow/templateflow.git
166+ RUN datalad get $TEMPLATEFLOW_HOME/tpl-MNI152NLin2009cAsym/*_T1w.nii.gz \
167+ $TEMPLATEFLOW_HOME/tpl-MNI152NLin2009cAsym/*_desc-brain_mask.nii.gz \
168+ $TEMPLATEFLOW_HOME/tpl-MNI152Lin/*_T1w.nii.gz \
169+ $TEMPLATEFLOW_HOME/tpl-MNI152Lin/*_desc-brain_mask.nii.gz \
170+ $TEMPLATEFLOW_HOME/tpl-OASIS30ANTs/*_T1w.nii.gz \
171+ $TEMPLATEFLOW_HOME/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_desc-brain_mask.nii.gz \
172+ $TEMPLATEFLOW_HOME/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_label-brain_probseg.nii.gz \
173+ $TEMPLATEFLOW_HOME/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_desc-BrainCerebellumExtraction_mask.nii.gz
163174
164175# Installing dev requirements (packages that are not in pypi)
165- ADD requirements.txt requirements.txt
176+ WORKDIR /src/
177+ COPY requirements.txt requirements.txt
166178RUN pip install -r requirements.txt && \
167179 rm -rf ~/.cache/pip
168180
169181# Installing FMRIPREP
170- COPY . /root/ src/fmriprep
182+ COPY . /src/fmriprep
171183ARG VERSION
172184# Force static versioning within container
173- RUN echo "${VERSION}" > /root/src/fmriprep/fmriprep/VERSION && \
174- cd /root/src/fmriprep && \
185+ RUN echo "${VERSION}" > /src/fmriprep/fmriprep/VERSION && \
186+ echo "include fmriprep/VERSION" >> /src/fmriprep/MANIFEST.in && \
187+ cd /src/fmriprep && \
175188 pip install .[all] && \
176189 rm -rf ~/.cache/pip
177190
178191RUN install -m 0755 \
179- /root/ src/fmriprep/scripts/generate_reference_mask.py \
192+ /src/fmriprep/scripts/generate_reference_mask.py \
180193 /usr/local/bin/generate_reference_mask
181194
182195ENV IS_DOCKER_8395080871=1
@@ -189,8 +202,8 @@ ARG BUILD_DATE
189202ARG VCS_REF
190203ARG VERSION
191204LABEL org.label-schema.build-date=$BUILD_DATE \
192- org.label-schema.name="FMRIPREP " \
193- org.label-schema.description="FMRIPREP - robust fMRI preprocessing tool" \
205+ org.label-schema.name="fMRIPrep " \
206+ org.label-schema.description="fMRIPrep - robust fMRI preprocessing tool" \
194207 org.label-schema.url="http://fmriprep.org" \
195208 org.label-schema.vcs-ref=$VCS_REF \
196209 org.label-schema.vcs-url="https://github.com/poldracklab/fmriprep" \
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