Merge pull request #60 from Shotgunosine/master

Allow lower resolution T2s
bids-apps · Jun 30, 2020 · c87c9c2 · c87c9c2
2 parents d51c7e4 + c0cfb22
commit c87c9c2
Show file tree

Hide file tree

Showing 4 changed files with 139 additions and 82 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -1,10 +1,10 @@
 # Generated by Neurodocker version 0.4.2-3-gf7055a1
-# Timestamp: 2020-06-04 13:51:08 UTC
-#
+# Timestamp: 2020-06-29 18:20:44 UTC
+# 
 # Thank you for using Neurodocker. If you discover any issues
 # or ways to improve this software, please submit an issue or
 # pull request on our GitHub repository:
-#
+# 
 #     https://github.com/kaczmarj/neurodocker
 
 FROM ubuntu:xenial
@@ -48,15 +48,12 @@ RUN apt-get update -qq \
            perl-modules \
            wget \
            curl \
-           python3 \
-           python3-pip \
-           python3-pandas \
-           python-pip \
            libsm-dev \
            libx11-dev \
            libxt-dev \
            libxext-dev \
            libglu1-mesa \
+           libpython2.7-stdlib \
     && apt-get clean \
     && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
@@ -91,7 +88,31 @@ RUN apt-get update -qq \
          --exclude='freesurfer/trctrain' \
     && sed -i '$isource "/opt/freesurfer/SetUpFreeSurfer.sh"' "$ND_ENTRYPOINT"
 
-RUN bash -c 'pip3 install nibabel pandas==0.21.0'
+ENV CONDA_DIR="/opt/miniconda-latest" \
+    PATH="/opt/miniconda-latest/bin:$PATH"
+RUN export PATH="/opt/miniconda-latest/bin:$PATH" \
+    && echo "Downloading Miniconda installer ..." \
+    && conda_installer="/tmp/miniconda.sh" \
+    && curl -fsSL --retry 5 -o "$conda_installer" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \
+    && bash "$conda_installer" -b -p /opt/miniconda-latest \
+    && rm -f "$conda_installer" \
+    && conda update -yq -nbase conda \
+    && conda config --system --prepend channels conda-forge \
+    && conda config --system --set auto_update_conda false \
+    && conda config --system --set show_channel_urls true \
+    && sync && conda clean -tipsy && sync \
+    && conda install -y -q --name base \
+           'python=3' \
+           'pip' \
+           'pandas' \
+           'setuptools' \
+           'pandas=0.21.0' \
+    && sync && conda clean -tipsy && sync \
+    && bash -c "source activate base \
+    &&   pip install --no-cache-dir  \
+             'nibabel'" \
+    && rm -rf ~/.cache/pip/* \
+    && sync
 
 RUN bash -c 'curl -sL https://deb.nodesource.com/setup_6.x | bash -'
 
@@ -111,8 +132,6 @@ ENV FSLDIR="/usr/share/fsl/5.0" \
     FSLTCLSH="/usr/bin/tclsh" \
     FSLWISH="/usr/bin/wish"
 
-RUN bash -c 'PATH=/usr/lib/fsl/5.0:$PATH'
-
 ENV OS="Linux" \
     FS_OVERRIDE="0" \
     FIX_VERTEX_AREA="" \
@@ -128,7 +147,7 @@ ENV OS="Linux" \
     FMRI_ANALYSIS_DIR="/opt/freesurfer/fsfast" \
     PERL5LIB="/opt/freesurfer/mni/share/perl5" \
     MNI_PERL5LIB="/opt/freesurfer/mni/share/perl5/" \
-    PATH="/opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin" \
+    PATH="/opt/miniconda-latest/bin:/opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/usr/lib/fsl/5.0:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin" \
     PYTHONPATH=""
 
 RUN mkdir root/matlab && touch root/matlab/startup.m
@@ -162,16 +181,12 @@ RUN echo '{ \
     \n        "perl-modules", \
     \n        "wget", \
     \n        "curl", \
-    \n        "python3", \
-    \n        "python3-pip", \
-    \n        "python3-pandas", \
-    \n        "python2.7", \
-    \n        "python-pip", \
     \n        "libsm-dev", \
     \n        "libx11-dev", \
     \n        "libxt-dev", \
     \n        "libxext-dev", \
-    \n        "libglu1-mesa" \
+    \n        "libglu1-mesa", \
+    \n        "libpython2.7-stdlib" \
     \n      ] \
     \n    ], \
     \n    [ \
@@ -182,8 +197,20 @@ RUN echo '{ \
     \n      } \
     \n    ], \
     \n    [ \
-    \n      "run_bash", \
-    \n      "pip3 install nibabel pandas==0.21.0" \
+    \n      "miniconda", \
+    \n      { \
+    \n        "use_env": "base", \
+    \n        "conda_install": [ \
+    \n          "python=3", \
+    \n          "pip", \
+    \n          "pandas", \
+    \n          "setuptools", \
+    \n          "pandas=0.21.0" \
+    \n        ], \
+    \n        "pip_install": [ \
+    \n          "nibabel" \
+    \n        ] \
+    \n      } \
     \n    ], \
     \n    [ \
     \n      "run_bash", \
@@ -212,10 +239,6 @@ RUN echo '{ \
     \n      } \
     \n    ], \
     \n    [ \
-    \n      "run_bash", \
-    \n      "PATH=/usr/lib/fsl/5.0:$PATH" \
-    \n    ], \
-    \n    [ \
     \n      "env", \
     \n      { \
     \n        "OS": "Linux", \
@@ -233,7 +256,7 @@ RUN echo '{ \
     \n        "FMRI_ANALYSIS_DIR": "/opt/freesurfer/fsfast", \
     \n        "PERL5LIB": "/opt/freesurfer/mni/share/perl5", \
     \n        "MNI_PERL5LIB": "/opt/freesurfer/mni/share/perl5/", \
-    \n        "PATH": "/opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin", \
+    \n        "PATH": "/opt/miniconda-latest/bin:/opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/usr/lib/fsl/5.0:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin", \
     \n        "PYTHONPATH": "" \
     \n      } \
     \n    ], \

diff --git a/Singularity b/Singularity
@@ -1,10 +1,10 @@
 # Generated by Neurodocker version 0.4.2-3-gf7055a1
-# Timestamp: 2020-06-04 13:51:09 UTC
-#
+# Timestamp: 2020-06-29 18:20:45 UTC
+# 
 # Thank you for using Neurodocker. If you discover any issues
 # or ways to improve this software, please submit an issue or
 # pull request on our GitHub repository:
-#
+# 
 #     https://github.com/kaczmarj/neurodocker
 
 Bootstrap: docker
@@ -43,15 +43,12 @@ apt-get install -y -q --no-install-recommends \
     perl-modules \
     wget \
     curl \
-    python3 \
-    python3-pip \
-    python3-pandas \
-    python-pip \
     libsm-dev \
     libx11-dev \
     libxt-dev \
     libxext-dev \
-    libglu1-mesa
+    libglu1-mesa \
+    libpython2.7-stdlib
 apt-get clean
 rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
@@ -84,7 +81,30 @@ curl -fsSL --retry 5 ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1/
   --exclude='freesurfer/trctrain'
 sed -i '$isource "/opt/freesurfer/SetUpFreeSurfer.sh"' "$ND_ENTRYPOINT"
 
-bash -c 'pip3 install nibabel pandas==0.21.0'
+export PATH="/opt/miniconda-latest/bin:$PATH"
+echo "Downloading Miniconda installer ..."
+conda_installer="/tmp/miniconda.sh"
+curl -fsSL --retry 5 -o "$conda_installer" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
+bash "$conda_installer" -b -p /opt/miniconda-latest
+rm -f "$conda_installer"
+conda update -yq -nbase conda
+conda config --system --prepend channels conda-forge
+conda config --system --set auto_update_conda false
+conda config --system --set show_channel_urls true
+sync && conda clean -tipsy && sync
+conda install -y -q --name base \
+    'python=3' \
+    'pip' \
+    'pandas' \
+    'setuptools' \
+    'pandas=0.21.0'
+sync && conda clean -tipsy && sync
+bash -c "source activate base
+  pip install --no-cache-dir  \
+      'nibabel'"
+rm -rf ~/.cache/pip/*
+sync
+
 
 bash -c 'curl -sL https://deb.nodesource.com/setup_6.x | bash -'
 
@@ -96,8 +116,6 @@ rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
 bash -c 'npm install -g [email protected]'
 
-bash -c 'PATH=/usr/lib/fsl/5.0:$PATH'
-
 mkdir root/matlab && touch root/matlab/startup.m
 
 mkdir /scratch
@@ -130,16 +148,12 @@ echo '{
 \n        "perl-modules",
 \n        "wget",
 \n        "curl",
-\n        "python3",
-\n        "python3-pip",
-\n        "python3-pandas",
-\n        "python2.7",
-\n        "python-pip",
 \n        "libsm-dev",
 \n        "libx11-dev",
 \n        "libxt-dev",
 \n        "libxext-dev",
-\n        "libglu1-mesa"
+\n        "libglu1-mesa",
+\n        "libpython2.7-stdlib"
 \n      ]
 \n    ],
 \n    [
@@ -150,8 +164,20 @@ echo '{
 \n      }
 \n    ],
 \n    [
-\n      "run_bash",
-\n      "pip3 install nibabel pandas==0.21.0"
+\n      "miniconda",
+\n      {
+\n        "use_env": "base",
+\n        "conda_install": [
+\n          "python=3",
+\n          "pip",
+\n          "pandas",
+\n          "setuptools",
+\n          "pandas=0.21.0"
+\n        ],
+\n        "pip_install": [
+\n          "nibabel"
+\n        ]
+\n      }
 \n    ],
 \n    [
 \n      "run_bash",
@@ -180,10 +206,6 @@ echo '{
 \n      }
 \n    ],
 \n    [
-\n      "run_bash",
-\n      "PATH=/usr/lib/fsl/5.0:$PATH"
-\n    ],
-\n    [
 \n      "env",
 \n      {
 \n        "OS": "Linux",
@@ -201,7 +223,7 @@ echo '{
 \n        "FMRI_ANALYSIS_DIR": "/opt/freesurfer/fsfast",
 \n        "PERL5LIB": "/opt/freesurfer/mni/share/perl5",
 \n        "MNI_PERL5LIB": "/opt/freesurfer/mni/share/perl5/",
-\n        "PATH": "/opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin",
+\n        "PATH": "/opt/miniconda-latest/bin:/opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/usr/lib/fsl/5.0:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin",
 \n        "PYTHONPATH": ""
 \n      }
 \n    ],
@@ -248,6 +270,8 @@ export LC_ALL="en_US.UTF-8"
 export ND_ENTRYPOINT="/neurodocker/startup.sh"
 export FREESURFER_HOME="/opt/freesurfer"
 export PATH="/opt/freesurfer/bin:$PATH"
+export CONDA_DIR="/opt/miniconda-latest"
+export PATH="/opt/miniconda-latest/bin:$PATH"
 export FSLDIR="/usr/share/fsl/5.0"
 export FSLOUTPUTTYPE="NIFTI_GZ"
 export FSLMULTIFILEQUIT="TRUE"
@@ -270,7 +294,7 @@ export MNI_DATAPATH="/opt/freesurfer/mni/data"
 export FMRI_ANALYSIS_DIR="/opt/freesurfer/fsfast"
 export PERL5LIB="/opt/freesurfer/mni/share/perl5"
 export MNI_PERL5LIB="/opt/freesurfer/mni/share/perl5/"
-export PATH="/opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin"
+export PATH="/opt/miniconda-latest/bin:/opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/usr/lib/fsl/5.0:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin"
 export PYTHONPATH=""
 
 %files

diff --git a/generate_freesurfer_images.sh b/generate_freesurfer_images.sh
@@ -46,24 +46,22 @@ docker run --rm ${image} generate docker \
   --base ubuntu:xenial \
   --pkg-manager apt \
   --install tcsh bc tar libgomp1 perl-modules wget curl \
-    python3 python3-pip python3-pandas python-pip \
-    libsm-dev libx11-dev libxt-dev libxext-dev libglu1-mesa \
+    libsm-dev libx11-dev libxt-dev libxext-dev libglu1-mesa libpython2.7-stdlib\
   --freesurfer version=6.0.1 install_path=/opt/freesurfer \
-  --run-bash 'pip3 install nibabel pandas==0.21.0' \
+  --miniconda use_env=base conda_install="python=3 pip pandas setuptools pandas=0.21.0" pip_install="nibabel" \
   --run-bash 'curl -sL https://deb.nodesource.com/setup_6.x | bash -' \
   --install nodejs \
   --run-bash 'npm install -g [email protected]' \
   --env FSLDIR=/usr/share/fsl/5.0 FSLOUTPUTTYPE=NIFTI_GZ \
         FSLMULTIFILEQUIT=TRUE POSSUMDIR=/usr/share/fsl/5.0 LD_LIBRARY_PATH=/usr/lib/fsl/5.0:$LD_LIBRARY_PATH \
         FSLTCLSH=/usr/bin/tclsh FSLWISH=/usr/bin/wish FSLOUTPUTTYPE=NIFTI_GZ \
-  --run-bash 'PATH=/usr/lib/fsl/5.0:$PATH' \
   --env OS=Linux FS_OVERRIDE=0 FIX_VERTEX_AREA= SUBJECTS_DIR=/opt/freesurfer/subjects \
         FSF_OUTPUT_FORMAT=nii.gz MNI_DIR=/opt/freesurfer/mni LOCAL_DIR=/opt/freesurfer/local \
         FREESURFER_HOME=/opt/freesurfer FSFAST_HOME=/opt/freesurfer/fsfast MINC_BIN_DIR=/opt/freesurfer/mni/bin \
         MINC_LIB_DIR=/opt/freesurfer/mni/lib MNI_DATAPATH=/opt/freesurfer/mni/data \
         FMRI_ANALYSIS_DIR=/opt/freesurfer/fsfast PERL5LIB=/opt/freesurfer/mni/share/perl5 \
         MNI_PERL5LIB=/opt/freesurfer/mni/share/perl5/ \
-        PATH=/opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin \
+        PATH=/opt/miniconda-latest/bin:/opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/usr/lib/fsl/5.0:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin \
         PYTHONPATH="" \
   --run 'mkdir root/matlab && touch root/matlab/startup.m' \
   --run 'mkdir /scratch' \
@@ -80,24 +78,22 @@ docker run --rm ${image} generate singularity \
   --base ubuntu:xenial \
   --pkg-manager apt \
   --install tcsh bc tar libgomp1 perl-modules wget curl \
-    python3 python3-pip python3-pandas python-pip \
-    libsm-dev libx11-dev libxt-dev libxext-dev libglu1-mesa \
+    libsm-dev libx11-dev libxt-dev libxext-dev libglu1-mesa libpython2.7-stdlib\
   --freesurfer version=6.0.1 install_path=/opt/freesurfer \
-  --run-bash 'pip3 install nibabel pandas==0.21.0' \
+  --miniconda use_env=base conda_install="python=3 pip pandas setuptools pandas=0.21.0" pip_install="nibabel" \
   --run-bash 'curl -sL https://deb.nodesource.com/setup_6.x | bash -' \
   --install nodejs \
   --run-bash 'npm install -g [email protected]' \
   --env FSLDIR=/usr/share/fsl/5.0 FSLOUTPUTTYPE=NIFTI_GZ \
         FSLMULTIFILEQUIT=TRUE POSSUMDIR=/usr/share/fsl/5.0 LD_LIBRARY_PATH=/usr/lib/fsl/5.0:$LD_LIBRARY_PATH \
         FSLTCLSH=/usr/bin/tclsh FSLWISH=/usr/bin/wish FSLOUTPUTTYPE=NIFTI_GZ \
-  --run-bash 'PATH=/usr/lib/fsl/5.0:$PATH' \
   --env OS=Linux FS_OVERRIDE=0 FIX_VERTEX_AREA= SUBJECTS_DIR=/opt/freesurfer/subjects \
         FSF_OUTPUT_FORMAT=nii.gz MNI_DIR=/opt/freesurfer/mni LOCAL_DIR=/opt/freesurfer/local \
         FREESURFER_HOME=/opt/freesurfer FSFAST_HOME=/opt/freesurfer/fsfast MINC_BIN_DIR=/opt/freesurfer/mni/bin \
         MINC_LIB_DIR=/opt/freesurfer/mni/lib MNI_DATAPATH=/opt/freesurfer/mni/data \
         FMRI_ANALYSIS_DIR=/opt/freesurfer/fsfast PERL5LIB=/opt/freesurfer/mni/share/perl5 \
         MNI_PERL5LIB=/opt/freesurfer/mni/share/perl5/ \
-        PATH=/opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin \
+        PATH=/opt/miniconda-latest/bin:/opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/usr/lib/fsl/5.0:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin \
         PYTHONPATH="" \
   --run 'mkdir root/matlab && touch root/matlab/startup.m' \
   --run 'mkdir /scratch' \