diff --git a/Dockerfile b/Dockerfile index e3b7280..11cd38b 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,5 +1,6 @@ -# Generated by Neurodocker version 0.5.0 -# Timestamp: 2020-09-16 16:07:32 UTC +# Your version: 0.6.0 Latest version: 0.7.0 +# Generated by Neurodocker version 0.6.0 +# Timestamp: 2021-04-13 14:10:53 UTC # # Thank you for using Neurodocker. If you discover any issues # or ways to improve this software, please submit an issue or @@ -72,17 +73,17 @@ RUN export PATH="/opt/miniconda-latest/bin:$PATH" \ && sync && conda clean --all && sync \ && conda create -y -q --name bidsonym \ && conda install -y -q --name bidsonym \ - 'python=3.6' \ - 'numpy' \ - 'nipype' \ - 'nibabel' \ - 'pandas' \ + "python=3.6" \ + "numpy" \ + "nipype" \ + "nibabel" \ + "pandas" \ && sync && conda clean --all && sync \ && bash -c "source activate bidsonym \ && pip install --no-cache-dir \ - 'deepdefacer' \ - 'tensorflow' \ - 'scikit-image'" \ + "deepdefacer" \ + "tensorflow" \ + "scikit-image"" \ && rm -rf ~/.cache/pip/* \ && sync \ && sed -i '$isource activate bidsonym' $ND_ENTRYPOINT diff --git a/Singularity b/Singularity deleted file mode 100644 index 5055759..0000000 --- a/Singularity +++ /dev/null @@ -1,105 +0,0 @@ -# Generated by Neurodocker version 0.5.0 -# Timestamp: 2020-09-16 16:07:33 UTC -# -# Thank you for using Neurodocker. If you discover any issues -# or ways to improve this software, please submit an issue or -# pull request on our GitHub repository: -# -# https://github.com/kaczmarj/neurodocker - -Bootstrap: docker -From: neurodebian:stretch-non-free - -%post -export ND_ENTRYPOINT="/neurodocker/startup.sh" -apt-get update -qq -apt-get install -y -q --no-install-recommends \ - apt-utils \ - bzip2 \ - ca-certificates \ - curl \ - locales \ - unzip -apt-get clean -rm -rf /var/lib/apt/lists/* -sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen -dpkg-reconfigure --frontend=noninteractive locales -update-locale LANG="en_US.UTF-8" -chmod 777 /opt && chmod a+s /opt -mkdir -p /neurodocker -if [ ! -f "$ND_ENTRYPOINT" ]; then - echo '#!/usr/bin/env bash' >> "$ND_ENTRYPOINT" - echo 'set -e' >> "$ND_ENTRYPOINT" - echo 'export USER="${USER:=`whoami`}"' >> "$ND_ENTRYPOINT" - echo 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT"; -fi -chmod -R 777 /neurodocker && chmod a+s /neurodocker - -apt-get update -qq -apt-get install -y -q --no-install-recommends \ - fsl-complete \ - git \ - num-utils \ - gcc \ - g++ \ - curl \ - build-essential -apt-get clean -rm -rf /var/lib/apt/lists/* - -bash -c 'curl -sL https://deb.nodesource.com/setup_10.x | bash - && apt-get install -y nodejs && apt-get install -y npm' - -sed -i '$isource /etc/fsl/fsl.sh' $ND_ENTRYPOINT - -export PATH="/opt/miniconda-latest/bin:$PATH" -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 "$conda_installer" -conda update -yq -nbase conda -conda config --system --prepend channels conda-forge -conda config --system --set auto_update_conda false -conda config --system --set show_channel_urls true -sync && conda clean --all && sync -conda create -y -q --name bidsonym -conda install -y -q --name bidsonym \ - 'python=3.6' \ - 'numpy' \ - 'nipype' \ - 'nibabel' \ - 'pandas' -sync && conda clean --all && sync -bash -c "source activate bidsonym - pip install --no-cache-dir \ - 'deepdefacer' \ - 'tensorflow' \ - 'scikit-image'" -rm -rf ~/.cache/pip/* -sync -sed -i '$isource activate bidsonym' $ND_ENTRYPOINT - - -bash -c 'source activate bidsonym && git clone https://github.com/poldracklab/pydeface.git && cd pydeface && python setup.py install && cd -' - -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 bids-validator@1.5.4' - -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/ \ No newline at end of file diff --git a/bidsonym/utils.py b/bidsonym/utils.py index d1255b8..b5c690d 100644 --- a/bidsonym/utils.py +++ b/bidsonym/utils.py @@ -113,6 +113,9 @@ def check_meta_data(bids_dir, subject_label, prob_fields=None): '_desc-headerinfo.csv'), index=False) + print('the following meta-data files will be checked:') + print(*list_meta_files, sep='\n') + for meta_file in list_meta_files: with open(meta_file, 'r') as json_file: diff --git a/generate_images.sh b/generate_images.sh index 41b11fd..2b56cf8 100644 --- a/generate_images.sh +++ b/generate_images.sh @@ -5,7 +5,7 @@ set -e generate_docker() { - docker run --rm kaczmarj/neurodocker:0.5.0 generate docker \ + docker run --rm kaczmarj/neurodocker:0.6.0 generate docker \ --base neurodebian:stretch-non-free \ --pkg-manager apt \ --install fsl-core git num-utils gcc g++ curl build-essential nano\ @@ -34,7 +34,7 @@ generate_docker() { } generate_singularity() { - docker run --rm kaczmarj/neurodocker:0.5.0 generate singularity \ + docker run --rm kaczmarj/neurodocker:0.6.0 generate singularity \ --base neurodebian:stretch-non-free \ --pkg-manager apt \ --install fsl-complete git num-utils gcc g++ curl build-essential\