update bidsvalidator

PeerHerholz · Aug 12, 2020 · 62e4616 · 62e4616
1 parent 8865235
commit 62e4616
Show file tree

Hide file tree

Showing 5 changed files with 105 additions and 46 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -1,5 +1,5 @@
 # Generated by Neurodocker version 0.5.0
-# Timestamp: 2019-11-08 16:38:08 UTC
+# Timestamp: 2020-08-12 21:15:26 UTC
 # 
 # Thank you for using Neurodocker. If you discover any issues
 # or ways to improve this software, please submit an issue or
@@ -52,7 +52,7 @@ RUN apt-get update -qq \
     && apt-get clean \
     && rm -rf /var/lib/apt/lists/*
 
-RUN bash -c 'curl -sL https://deb.nodesource.com/setup_8.x | bash - && apt-get install -y nodejs && apt-get install -y npm'
+RUN bash -c 'curl -sL https://deb.nodesource.com/setup_10.x | bash - && apt-get install -y nodejs && apt-get install -y npm'
 
 RUN sed -i '$isource /etc/fsl/fsl.sh' $ND_ENTRYPOINT
 
@@ -63,7 +63,7 @@ ENV FSLDIR="/usr/share/fsl/5.0" \
     LD_LIBRARY_PATH="/usr/lib/fsl/5.0:" \
     FSLTCLSH="/usr/bin/tclsh" \
     FSLWISH="/usr/bin/wish" \
-    PATH="/usr/lib/fsl/5.0:/Users/peerherholz/abin:/usr/local/antsbin/bin:/Applications/MATLAB_R2014a.app/bin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/usr/local/fsl/bin:/Users/peerherholz/anaconda3/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/Applications/workbench/bin_macosx64:/usr/local/texlive/2019/bin/x86_64-darwin"
+    PATH="/usr/lib/fsl/5.0:/Users/peerherholz/anaconda3/bin:/Users/peerherholz/anaconda3/condabin:/Users/peerherholz/abin:/usr/local/antsbin/bin:/Applications/MATLAB_R2014a.app/bin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/usr/local/fsl/bin:/Users/peerherholz/anaconda3/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/Applications/workbench/bin_macosx64:/usr/local/texlive/2019/bin/x86_64-darwin"
 
 ENV CONDA_DIR="/opt/miniconda-latest" \
     PATH="/opt/miniconda-latest/bin:$PATH"
@@ -109,7 +109,7 @@ ENV MRIDEFACER_DATA_DIR="/mridefacer/data"
 
 RUN bash -c 'rm -r /usr/share/fsl/data/atlases && rm -r /usr/share/fsl/data/first && rm -r /usr/share/fsl/data/possum'
 
-RUN bash -c 'npm install -g bids-validator@1.2.3'
+RUN bash -c 'npm install -g bids-validator@1.5.4'
 
 RUN bash -c 'mkdir /home/mri-deface-detector && cd /home/mri-deface-detector && npm install sharp --unsafe-perm && npm install -g mri-deface-detector --unsafe-perm && cd ~'
 
@@ -150,7 +150,7 @@ RUN echo '{ \
     \n    ], \
     \n    [ \
     \n      "run_bash", \
-    \n      "curl -sL https://deb.nodesource.com/setup_8.x | bash - && apt-get install -y nodejs && apt-get install -y npm" \
+    \n      "curl -sL https://deb.nodesource.com/setup_10.x | bash - && apt-get install -y nodejs && apt-get install -y npm" \
     \n    ], \
     \n    [ \
     \n      "add_to_entrypoint", \
@@ -166,7 +166,7 @@ RUN echo '{ \
     \n        "LD_LIBRARY_PATH": "/usr/lib/fsl/5.0:", \
     \n        "FSLTCLSH": "/usr/bin/tclsh", \
     \n        "FSLWISH": "/usr/bin/wish", \
-    \n        "PATH": "/usr/lib/fsl/5.0:/Users/peerherholz/abin:/usr/local/antsbin/bin:/Applications/MATLAB_R2014a.app/bin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/usr/local/fsl/bin:/Users/peerherholz/anaconda3/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/Applications/workbench/bin_macosx64:/usr/local/texlive/2019/bin/x86_64-darwin" \
+    \n        "PATH": "/usr/lib/fsl/5.0:/Users/peerherholz/anaconda3/bin:/Users/peerherholz/anaconda3/condabin:/Users/peerherholz/abin:/usr/local/antsbin/bin:/Applications/MATLAB_R2014a.app/bin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/usr/local/fsl/bin:/Users/peerherholz/anaconda3/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/Applications/workbench/bin_macosx64:/usr/local/texlive/2019/bin/x86_64-darwin" \
     \n      } \
     \n    ], \
     \n    [ \
@@ -220,7 +220,7 @@ RUN echo '{ \
     \n    ], \
     \n    [ \
     \n      "run_bash", \
-    \n      "npm install -g bids-validator@1.2.3" \
+    \n      "npm install -g bids-validator@1.5.4" \
     \n    ], \
     \n    [ \
     \n      "run_bash", \

diff --git a/Singularity b/Singularity
@@ -1,5 +1,5 @@
 # Generated by Neurodocker version 0.5.0
-# Timestamp: 2019-11-08 16:38:11 UTC
+# Timestamp: 2020-08-12 21:15:27 UTC
 # 
 # Thank you for using Neurodocker. If you discover any issues
 # or ways to improve this software, please submit an issue or
@@ -40,10 +40,15 @@ apt-get install -y -q --no-install-recommends \
     fsl-complete \
     git \
     num-utils \
-    gcc
+    gcc \
+    g++ \
+    curl \
+    build-essential
 apt-get clean
 rm -rf /var/lib/apt/lists/*
 
+bash -c 'curl -sL https://deb.nodesource.com/setup_10.x | bash - && apt-get install -y nodejs && apt-get install -y npm'
+
 sed -i '$isource /etc/fsl/fsl.sh' $ND_ENTRYPOINT
 
 export PATH="/opt/miniconda-latest/bin:$PATH"
@@ -68,8 +73,8 @@ sync && conda clean --all && sync
 bash -c "source activate bidsonym
   pip install --no-cache-dir  \
       'deepdefacer' \
-      'nobrainer' \
-      'tensorflow'"
+      'tensorflow' \
+      'scikit-image'"
 rm -rf ~/.cache/pip/*
 sync
 sed -i '$isource activate bidsonym' $ND_ENTRYPOINT
@@ -79,14 +84,26 @@ bash -c 'source activate bidsonym && git clone https://github.com/poldracklab/py
 
 bash -c 'source activate bidsonym && git clone https://github.com/nipy/quickshear.git  && cd quickshear && python setup.py install && cd -'
 
+bash -c 'source activate bidsonym && git clone https://github.com/neuronets/nobrainer.git  && cd nobrainer && python setup.py install && cd -'
+
+bash -c 'mkdir -p /opt/nobrainer/models && cd /opt/nobrainer/models && curl -LJO  https://github.com/neuronets/nobrainer-models/releases/download/0.1/brain-extraction-unet-128iso-model.h5 && cd ~ '
+
 bash -c 'git clone https://github.com/mih/mridefacer'
 
 bash -c 'rm -r /usr/share/fsl/data/atlases && rm -r /usr/share/fsl/data/first && rm -r /usr/share/fsl/data/possum'
 
+bash -c 'npm install -g [email protected]'
+
+bash -c 'mkdir /home/mri-deface-detector && cd /home/mri-deface-detector && npm install sharp --unsafe-perm && npm install -g mri-deface-detector --unsafe-perm && cd ~'
+
+bash -c 'git clone https://github.com/miykael/gif_your_nifti && cd gif_your_nifti && source activate bidsonym && python setup.py install'
+
 bash -c 'chmod a+x /home/bm/bidsonym/fs_data/mri_deface'
 
 bash -c 'source activate bidsonym && cd /home/bm && pip install -e .'
 
+cd /tmp/
+
 echo '{
 \n  "pkg_manager": "apt",
 \n  "instructions": [
@@ -107,10 +124,17 @@ echo '{
 \n        "fsl-complete",
 \n        "git",
 \n        "num-utils",
-\n        "gcc"
+\n        "gcc",
+\n        "g++",
+\n        "curl",
+\n        "build-essential"
 \n      ]
 \n    ],
 \n    [
+\n      "run_bash",
+\n      "curl -sL https://deb.nodesource.com/setup_10.x | bash - && apt-get install -y nodejs && apt-get install -y npm"
+\n    ],
+\n    [
 \n      "add_to_entrypoint",
 \n      "source /etc/fsl/fsl.sh"
 \n    ],
@@ -124,7 +148,7 @@ echo '{
 \n        "LD_LIBRARY_PATH": "/usr/lib/fsl/5.0:",
 \n        "FSLTCLSH": "/usr/bin/tclsh",
 \n        "FSLWISH": "/usr/bin/wish",
-\n        "PATH": "/usr/lib/fsl/5.0:/Users/peerherholz/abin:/usr/local/antsbin/bin:/Applications/MATLAB_R2014a.app/bin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/usr/local/fsl/bin:/Users/peerherholz/anaconda3/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/Applications/workbench/bin_macosx64:/usr/local/texlive/2019/bin/x86_64-darwin"
+\n        "PATH": "/usr/lib/fsl/5.0:/Users/peerherholz/anaconda3/bin:/Users/peerherholz/anaconda3/condabin:/Users/peerherholz/abin:/usr/local/antsbin/bin:/Applications/MATLAB_R2014a.app/bin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/usr/local/fsl/bin:/Users/peerherholz/anaconda3/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/Applications/workbench/bin_macosx64:/usr/local/texlive/2019/bin/x86_64-darwin"
 \n      }
 \n    ],
 \n    [
@@ -139,8 +163,8 @@ echo '{
 \n        ],
 \n        "pip_install": [
 \n          "deepdefacer",
-\n          "nobrainer",
-\n          "tensorflow"
+\n          "tensorflow",
+\n          "scikit-image"
 \n        ],
 \n        "create_env": "bidsonym",
 \n        "activate": true
@@ -156,6 +180,14 @@ echo '{
 \n    ],
 \n    [
 \n      "run_bash",
+\n      "source activate bidsonym && git clone https://github.com/neuronets/nobrainer.git  && cd nobrainer && python setup.py install && cd -"
+\n    ],
+\n    [
+\n      "run_bash",
+\n      "mkdir -p /opt/nobrainer/models && cd /opt/nobrainer/models && curl -LJO  https://github.com/neuronets/nobrainer-models/releases/download/0.1/brain-extraction-unet-128iso-model.h5 && cd ~ "
+\n    ],
+\n    [
+\n      "run_bash",
 \n      "git clone https://github.com/mih/mridefacer"
 \n    ],
 \n    [
@@ -169,6 +201,18 @@ echo '{
 \n      "rm -r /usr/share/fsl/data/atlases && rm -r /usr/share/fsl/data/first && rm -r /usr/share/fsl/data/possum"
 \n    ],
 \n    [
+\n      "run_bash",
+\n      "npm install -g [email protected]"
+\n    ],
+\n    [
+\n      "run_bash",
+\n      "mkdir /home/mri-deface-detector && cd /home/mri-deface-detector && npm install sharp --unsafe-perm && npm install -g mri-deface-detector --unsafe-perm && cd ~"
+\n    ],
+\n    [
+\n      "run_bash",
+\n      "git clone https://github.com/miykael/gif_your_nifti && cd gif_your_nifti && source activate bidsonym && python setup.py install"
+\n    ],
+\n    [
 \n      "copy",
 \n      [
 \n        ".",
@@ -197,6 +241,10 @@ echo '{
 \n      }
 \n    ],
 \n    [
+\n      "workdir",
+\n      "/tmp/"
+\n    ],
+\n    [
 \n      "entrypoint",
 \n      "/neurodocker/startup.sh  bidsonym"
 \n    ]
@@ -214,7 +262,7 @@ export POSSUMDIR="/usr/share/fsl/5.0"
 export LD_LIBRARY_PATH="/usr/lib/fsl/5.0:"
 export FSLTCLSH="/usr/bin/tclsh"
 export FSLWISH="/usr/bin/wish"
-export PATH="/usr/lib/fsl/5.0:/Users/peerherholz/abin:/usr/local/antsbin/bin:/Applications/MATLAB_R2014a.app/bin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/usr/local/fsl/bin:/Users/peerherholz/anaconda3/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/Applications/workbench/bin_macosx64:/usr/local/texlive/2019/bin/x86_64-darwin"
+export PATH="/usr/lib/fsl/5.0:/Users/peerherholz/anaconda3/bin:/Users/peerherholz/anaconda3/condabin:/Users/peerherholz/abin:/usr/local/antsbin/bin:/Applications/MATLAB_R2014a.app/bin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/usr/local/fsl/bin:/Users/peerherholz/anaconda3/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/Applications/workbench/bin_macosx64:/usr/local/texlive/2019/bin/x86_64-darwin"
 export CONDA_DIR="/opt/miniconda-latest"
 export PATH="/opt/miniconda-latest/bin:$PATH"
 export MRIDEFACER_DATA_DIR="/mridefacer/data"

diff --git a/bidsonym/run_deeid.py b/bidsonym/run_deeid.py
@@ -8,6 +8,7 @@
                             run_brain_extraction_nb, run_brain_extraction_bet, validate_input_dir)
 from bids import BIDSLayout
 
+
 def get_parser():
 
     __version__ = open(os.path.join(os.path.dirname(os.path.realpath(__file__)),
@@ -97,7 +98,6 @@ def run_deeid():
                         "This refers to:")
         print(list_part_prob)
 
-
     list_check_meta = args.check_meta
 
     list_field_del = args.del_meta

diff --git a/bidsonym/utils.py b/bidsonym/utils.py
@@ -293,3 +293,7 @@ def deface_t2w(image, warped_mask, outfile):
     masked_brain = Nifti1Image(outdata, infile_img.get_affine(),
                                infile_img.get_header())
     masked_brain.to_filename(outfile)
+
+
+
+
diff --git a/generate_images.sh b/generate_images.sh
@@ -13,7 +13,7 @@ generate_docker() {
              --base neurodebian:stretch-non-free \
              --pkg-manager apt \
              --install fsl-complete git num-utils gcc g++ curl build-essential\
-             --run-bash "curl -sL https://deb.nodesource.com/setup_8.x | bash - && apt-get install -y nodejs && apt-get install -y npm"\
+             --run-bash "curl -sL https://deb.nodesource.com/setup_10.x | bash - && apt-get install -y nodejs && apt-get install -y npm"\
              --add-to-entrypoint "source /etc/fsl/fsl.sh" \
              --env FSLDIR=/usr/share/fsl/5.0 \
                    FSLOUTPUTTYPE=NIFTI_GZ \
@@ -35,7 +35,7 @@ generate_docker() {
              --run-bash "git clone https://github.com/mih/mridefacer" \
              --env MRIDEFACER_DATA_DIR=/mridefacer/data \
              --run-bash "rm -r /usr/share/fsl/data/atlases && rm -r /usr/share/fsl/data/first && rm -r /usr/share/fsl/data/possum" \
-             --run-bash "npm install -g bids-validator@1.2.3" \
+             --run-bash "npm install -g bids-validator@1.5.4" \
              --run-bash "mkdir /home/mri-deface-detector && cd /home/mri-deface-detector && npm install sharp --unsafe-perm && npm install -g mri-deface-detector --unsafe-perm && cd ~" \
              --run-bash "git clone https://github.com/miykael/gif_your_nifti && cd gif_your_nifti && source activate bidsonym && python setup.py install" \
              --copy . /home/bm \
@@ -49,34 +49,41 @@ generate_docker() {
 
 generate_singularity() {
   docker run --rm kaczmarj/neurodocker:0.5.0 generate singularity \
-            --base neurodebian:stretch-non-free \
-            --pkg-manager apt \
-            --install fsl-complete git num-utils gcc \
-            --add-to-entrypoint "source /etc/fsl/fsl.sh" \
-            --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:$LD_LIBRARY_PATH \
-                  FSLTCLSH=/usr/bin/tclsh \
-                  FSLWISH=/usr/bin/wish \
-                  PATH=/usr/lib/fsl/5.0:$PATH \
+             --base neurodebian:stretch-non-free \
+             --pkg-manager apt \
+             --install fsl-complete git num-utils gcc g++ curl build-essential\
+             --run-bash "curl -sL https://deb.nodesource.com/setup_10.x | bash - && apt-get install -y nodejs && apt-get install -y npm"\
+             --add-to-entrypoint "source /etc/fsl/fsl.sh" \
+             --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:$LD_LIBRARY_PATH \
+                   FSLTCLSH=/usr/bin/tclsh \
+                   FSLWISH=/usr/bin/wish \
+                   PATH=/usr/lib/fsl/5.0:$PATH \
             --miniconda \
-               conda_install="python=3.6 numpy nipype nibabel pandas" \
-               pip_install='deepdefacer nobrainer tensorflow' \
-               create_env='bidsonym' \
-               activate=true \
-            --run-bash "source activate bidsonym && git clone https://github.com/poldracklab/pydeface.git && cd pydeface && python setup.py install && cd -" \
-            --run-bash "source activate bidsonym && git clone https://github.com/nipy/quickshear.git  && cd quickshear && python setup.py install && cd -" \
-            --run-bash "git clone https://github.com/mih/mridefacer" \
-            --env MRIDEFACER_DATA_DIR=/mridefacer/data \
-            --run-bash "rm -r /usr/share/fsl/data/atlases && rm -r /usr/share/fsl/data/first && rm -r /usr/share/fsl/data/possum" \
-            --copy . /home/bm \
-            --run-bash "chmod a+x /home/bm/bidsonym/fs_data/mri_deface" \
-            --run-bash "source activate bidsonym && cd /home/bm && pip install -e ." \
-            --copy example_data /home/bidsonym/example_data \
-            --env IS_DOCKER=1 \
-            --entrypoint "/neurodocker/startup.sh  bidsonym"
+                conda_install="python=3.6 numpy nipype nibabel pandas" \
+                pip_install='deepdefacer tensorflow scikit-image' \
+                create_env='bidsonym' \
+                activate=true \
+             --run-bash "source activate bidsonym && git clone https://github.com/poldracklab/pydeface.git && cd pydeface && python setup.py install && cd -" \
+             --run-bash "source activate bidsonym && git clone https://github.com/nipy/quickshear.git  && cd quickshear && python setup.py install && cd -" \
+             --run-bash "source activate bidsonym && git clone https://github.com/neuronets/nobrainer.git  && cd nobrainer && python setup.py install && cd -" \
+             --run-bash "mkdir -p /opt/nobrainer/models && cd /opt/nobrainer/models && curl -LJO  https://github.com/neuronets/nobrainer-models/releases/download/0.1/brain-extraction-unet-128iso-model.h5 && cd ~ " \
+             --run-bash "git clone https://github.com/mih/mridefacer" \
+             --env MRIDEFACER_DATA_DIR=/mridefacer/data \
+             --run-bash "rm -r /usr/share/fsl/data/atlases && rm -r /usr/share/fsl/data/first && rm -r /usr/share/fsl/data/possum" \
+             --run-bash "npm install -g [email protected]" \
+             --run-bash "mkdir /home/mri-deface-detector && cd /home/mri-deface-detector && npm install sharp --unsafe-perm && npm install -g mri-deface-detector --unsafe-perm && cd ~" \
+             --run-bash "git clone https://github.com/miykael/gif_your_nifti && cd gif_your_nifti && source activate bidsonym && python setup.py install" \
+             --copy . /home/bm \
+             --run-bash "chmod a+x /home/bm/bidsonym/fs_data/mri_deface" \
+             --run-bash "source activate bidsonym && cd /home/bm && pip install -e ." \
+             --copy example_data /home/bidsonym/example_data \
+             --env IS_DOCKER=1 \
+             --workdir '/tmp/' \
+             --entrypoint "/neurodocker/startup.sh  bidsonym"
 }
 
 # generate files
Original file line number	Diff line number	Diff line change
Expand Up		@@ -293,3 +293,7 @@ def deface_t2w(image, warped_mask, outfile):
		masked_brain = Nifti1Image(outdata, infile_img.get_affine(),
		infile_img.get_header())
		masked_brain.to_filename(outfile)