pennlinc
    xcp_d
    0.8.1
Namespace
pennlinc
Image / Tag
xcp_d:0.8.1
Content Digest
sha256:ca48fdd72c347735790434f46857541d400d3cb6b4815b0be025e6b3ab15842d
Details
Created

2024-08-16 18:57:47 UTC

Size

6.32 GB

Content Digest
Labels
  • org.label-schema.build-date
    2024-08-16T18:56:26Z
  • org.label-schema.description
    xcp_d- postprocessing of fmriprep outputs
  • org.label-schema.name
    xcp_d
  • org.label-schema.schema-version
    1.0
  • org.label-schema.url
    https://xcp-d.readthedocs.io/
  • org.label-schema.vcs-ref
    7a8f9ba
  • org.label-schema.vcs-url
    https://github.com/PennLINC/xcp_d
  • org.label-schema.version
    0.8.1
Environment
AFNI_IMSAVE_WARNINGS

NO

AFNI_MODELPATH

/usr/lib/afni/models

AFNI_PLUGINPATH

/usr/lib/afni/plugins

AFNI_TTATLAS_DATASET

/usr/share/afni/atlases

ANTSPATH

/usr/lib/ants

C3DPATH

/opt/c3d/bin

CPATH

/usr/local/miniconda/include:

FIX_VERTEX_AREA

FREESURFER_HOME

/opt/freesurfer

FSF_OUTPUT_FORMAT

nii.gz

FSLDIR

/opt/fsl

FSLGECUDAQ

cuda.q

FSLLOCKDIR

FSLMACHINELIST

FSLMULTIFILEQUIT

TRUE

FSLOUTPUTTYPE

NIFTI_GZ

FSLREMOTECALL

FSL_DEPS

libquadmath0;libnewimage.so;libmiscmaths.so

FUNCTIONALS_DIR

/opt/freesurfer/sessions

HOME

/home/xcp_d

LANG

C.UTF-8

LC_ALL

C.UTF-8

LD_LIBRARY_PATH

/opt/fsl/lib:

LOCAL_DIR

/opt/freesurfer/local

MINC_BIN_DIR

/opt/freesurfer/mni/bin

MINC_LIB_DIR

/opt/freesurfer/mni/lib

MKL_NUM_THREADS

1

MNI_DATAPATH

/opt/freesurfer/mni/data

MNI_DIR

/opt/freesurfer/mni

MNI_PERL5LIB

/opt/freesurfer/mni/lib/perl5/5.8.5

OMP_NUM_THREADS

1

OS

Linux

PATH

/usr/lib/ants:/opt/freesurfer/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/opt/fsl/lib:/opt/fsl/bin:/opt/c3d/bin:/usr/lib/afni/bin:/usr/local/miniconda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

PERL5LIB

/opt/freesurfer/mni/lib/perl5/5.8.5

PYTHONNOUSERSITE

1

SUBJECTS_DIR

/opt/freesurfer/subjects

Layers

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History
2022-06-06 22:21:04 UTC

/bin/sh -c #(nop) ADD file:40290d9a94ae76c35ab1f57178130ce1c5b976e34a91e77472ecf7e945ab64f9 in /

2022-06-06 22:21:05 UTC

/bin/sh -c #(nop) CMD ["bash"]

2024-04-23 21:49:06 UTC (buildkit.dockerfile.v0)

COPY docker/files/neurodebian.gpg /usr/local/etc/neurodebian.gpg # buildkit

2024-04-23 21:49:06 UTC (buildkit.dockerfile.v0)

RUN /bin/sh -c mkdir /AtlasPack # buildkit

2024-04-23 21:49:06 UTC (buildkit.dockerfile.v0)

COPY /AtlasPack/tpl-fsLR_*.dlabel.nii /AtlasPack/ # buildkit

2024-04-23 21:49:06 UTC (buildkit.dockerfile.v0)

COPY /AtlasPack/tpl-MNI152NLin6Asym_*.nii.gz /AtlasPack/ # buildkit

2024-04-23 21:49:06 UTC (buildkit.dockerfile.v0)

COPY /AtlasPack/atlas-4S*.tsv /AtlasPack/ # buildkit

2024-04-23 21:49:06 UTC (buildkit.dockerfile.v0)

COPY /AtlasPack/*.json /AtlasPack/ # buildkit

2024-04-23 21:51:25 UTC (buildkit.dockerfile.v0)

RUN /bin/sh -c apt-get update && apt-get install -y --no-install-recommends apt-utils autoconf build-essential bzip2 ca-certificates curl dc git graphviz libtool locales pandoc pandoc-citeproc pkg-config unzip wget xvfb && curl -sSL https://deb.nodesource.com/setup_17.x | bash - && apt-get install -y --no-install-recommends nodejs && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* # buildkit

2024-04-23 21:51:32 UTC (buildkit.dockerfile.v0)

ENV OS=Linux FIX_VERTEX_AREA=

2024-04-23 21:51:32 UTC (buildkit.dockerfile.v0)

RUN /bin/sh -c curl -sSLO https://repo.continuum.io/miniconda/Miniconda3-py310_23.10.0-1-Linux-x86_64.sh && bash Miniconda3-py310_23.10.0-1-Linux-x86_64.sh -b -p /usr/local/miniconda && rm Miniconda3-py310_23.10.0-1-Linux-x86_64.sh # buildkit

2024-04-23 21:51:32 UTC (buildkit.dockerfile.v0)

ENV PATH=/usr/local/miniconda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin CPATH=/usr/local/miniconda/include: LANG=C.UTF-8 LC_ALL=C.UTF-8 PYTHONNOUSERSITE=1

2024-04-23 21:53:51 UTC (buildkit.dockerfile.v0)

RUN /bin/sh -c conda install -y python=3.10 libxslt=1.1 mkl=2021.2 mkl-service=2.3 numpy=1.18.1 pandas=1.2 scikit-learn=0.24 scipy=1.6 traits=6.2 zstd=1.4; sync && pip install matplotlib requests templateflow ; sync && chmod -R a+rX /usr/local/miniconda; sync && chmod +x /usr/local/miniconda/bin/*; sync && conda build purge-all; sync && conda clean -tipsy; sync # buildkit

2024-04-23 21:53:54 UTC (buildkit.dockerfile.v0)

RUN /bin/sh -c curl -sSL "http://neuro.debian.net/lists/$( lsb_release -c | cut -f2 ).us-ca.full" >> /etc/apt/sources.list.d/neurodebian.sources.list && apt-key add /usr/local/etc/neurodebian.gpg && (apt-key adv --refresh-keys --keyserver hkp://ha.pool.sks-keyservers.net 0xA5D32F012649A5A9 || true) # buildkit

2024-04-23 21:54:32 UTC (buildkit.dockerfile.v0)

RUN /bin/sh -c apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends afni=18.0.05+git24-gb25b21054~dfsg.1-1~nd17.10+1+nd18.04+1 connectome-workbench=1.5.0-1~nd18.04+1 git-annex-standalone && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* # buildkit

2024-04-23 21:54:32 UTC (buildkit.dockerfile.v0)

ENV AFNI_MODELPATH=/usr/lib/afni/models AFNI_IMSAVE_WARNINGS=NO AFNI_TTATLAS_DATASET=/usr/share/afni/atlases AFNI_PLUGINPATH=/usr/lib/afni/plugins

2024-04-23 21:54:32 UTC (buildkit.dockerfile.v0)

ENV PATH=/usr/lib/afni/bin:/usr/local/miniconda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

2024-04-23 21:54:42 UTC (buildkit.dockerfile.v0)

RUN /bin/sh -c echo "Downloading C3D ..." && mkdir /opt/c3d && curl -sSL --retry 5 https://sourceforge.net/projects/c3d/files/c3d/1.0.0/c3d-1.0.0-Linux-x86_64.tar.gz/download | tar -xzC /opt/c3d --strip-components=1 # buildkit

2024-04-23 21:54:42 UTC (buildkit.dockerfile.v0)

ENV C3DPATH=/opt/c3d/bin PATH=/opt/c3d/bin:/usr/lib/afni/bin:/usr/local/miniconda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

2024-04-23 21:54:42 UTC (buildkit.dockerfile.v0)

COPY /usr/lib/fsl/5.0/slicer /opt/fsl/lib/slicer # buildkit

2024-04-23 21:54:42 UTC (buildkit.dockerfile.v0)

COPY /usr/lib/fsl/5.0/slicesdir /opt/fsl/lib/slicesdir # buildkit

2024-04-23 21:54:42 UTC (buildkit.dockerfile.v0)

COPY /usr/lib/fsl/5.0/pngappend /opt/fsl/lib/pngappend # buildkit

2024-04-23 21:54:42 UTC (buildkit.dockerfile.v0)

COPY /usr/lib/fsl/5.0/remove_ext /opt/fsl/lib/remove_ext # buildkit

2024-04-23 21:54:42 UTC (buildkit.dockerfile.v0)

COPY /usr/bin/fsl5.0-slicer /opt/fsl/bin/fsl-5.0-slicer # buildkit

2024-04-23 21:54:42 UTC (buildkit.dockerfile.v0)

COPY /usr/bin/fsl5.0-slicesdir /opt/fsl/bin/fsl5.0-slicesdir # buildkit

2024-04-23 21:54:42 UTC (buildkit.dockerfile.v0)

COPY /usr/bin/fsl5.0-pngappend /opt/fsl/bin/fsl5.0-pngappend # buildkit

2024-04-23 21:54:42 UTC (buildkit.dockerfile.v0)

COPY /usr/bin/fsl5.0-remove_ext /opt/fsl/bin/fsl5.0-remove_ext # buildkit

2024-04-23 21:54:42 UTC (buildkit.dockerfile.v0)

COPY /usr/share/fsl/5.0/bin/slicer /opt/fsl/bin/slicer # buildkit

2024-04-23 21:54:42 UTC (buildkit.dockerfile.v0)

COPY /usr/share/fsl/5.0/bin/slicesdir /opt/fsl/bin/slicesdir # buildkit

2024-04-23 21:54:42 UTC (buildkit.dockerfile.v0)

COPY /usr/share/fsl/5.0/bin/pngappend /opt/fsl/bin/pngappend # buildkit

2024-04-23 21:54:42 UTC (buildkit.dockerfile.v0)

COPY /usr/share/fsl/5.0/bin/remove_ext /opt/fsl/bin/remove_ext # buildkit

2024-04-23 21:54:42 UTC (buildkit.dockerfile.v0)

COPY /usr/lib/fsl/5.0/libnewimage.so /opt/fsl/lib/libnewimage.so # buildkit

2024-04-23 21:54:42 UTC (buildkit.dockerfile.v0)

COPY /usr/lib/fsl/5.0/libmiscmaths.so /opt/fsl/lib/libmiscmaths.so # buildkit

2024-04-23 21:54:42 UTC (buildkit.dockerfile.v0)

COPY /usr/lib/fsl/5.0/libmiscpic.so /opt/fsl/lib/libmiscpic.so # buildkit

2024-04-23 21:54:42 UTC (buildkit.dockerfile.v0)

COPY /usr/lib/fsl/5.0/libfslio.so /opt/fsl/lib/libfslio.so # buildkit

2024-04-23 21:54:42 UTC (buildkit.dockerfile.v0)

COPY /usr/lib/fsl/5.0/libutils.so /opt/fsl/lib/libutils.so # buildkit

2024-04-23 21:54:42 UTC (buildkit.dockerfile.v0)

COPY /usr/lib/fsl/5.0/libprob.so /opt/fsl/lib/libprob.so # buildkit

2024-04-23 21:54:42 UTC (buildkit.dockerfile.v0)

COPY /usr/lib/libnewmat.so.10.0.0 /opt/fsl/lib/libnewmat.so.10 # buildkit

2024-04-23 21:54:42 UTC (buildkit.dockerfile.v0)

COPY /usr/lib/fsl/5.0/applywarp /opt/fsl/lib/applywarp # buildkit

2024-04-23 21:54:42 UTC (buildkit.dockerfile.v0)

ENV FSLDIR=/opt/fsl FSLOUTPUTTYPE=NIFTI_GZ FSLMULTIFILEQUIT=TRUE FSLLOCKDIR= FSLMACHINELIST= FSLREMOTECALL= FSLGECUDAQ=cuda.q LD_LIBRARY_PATH=/opt/fsl/lib: PATH=/opt/fsl/lib:/opt/fsl/bin:/opt/c3d/bin:/usr/lib/afni/bin:/usr/local/miniconda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin FSL_DEPS=libquadmath0;libnewimage.so;libmiscmaths.so

2024-04-23 21:59:01 UTC (buildkit.dockerfile.v0)

RUN /bin/sh -c 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 --exclude="freesurfer/diffusion" --exclude="freesurfer/docs" --exclude="freesurfer/fsfast" --exclude="freesurfer/lib/cuda" --exclude="freesurfer/lib/qt" --exclude="freesurfer/matlab" --exclude="freesurfer/mni/share/man" --exclude="freesurfer/subjects/fsaverage_sym" --exclude="freesurfer/subjects/fsaverage3" --exclude="freesurfer/subjects/fsaverage4" --exclude="freesurfer/subjects/cvs_avg35" --exclude="freesurfer/subjects/cvs_avg35_inMNI152" --exclude="freesurfer/subjects/bert" --exclude="freesurfer/subjects/lh.EC_average" --exclude="freesurfer/subjects/rh.EC_average" --exclude="freesurfer/subjects/sample-*.mgz" --exclude="freesurfer/subjects/V1_average" --exclude="freesurfer/trctrain" # buildkit

2024-04-23 21:59:01 UTC (buildkit.dockerfile.v0)

ENV FREESURFER_HOME=/opt/freesurfer FSF_OUTPUT_FORMAT=nii.gz

2024-04-23 21:59:01 UTC (buildkit.dockerfile.v0)

ENV FUNCTIONALS_DIR=/opt/freesurfer/sessions LOCAL_DIR=/opt/freesurfer/local MINC_BIN_DIR=/opt/freesurfer/mni/bin MINC_LIB_DIR=/opt/freesurfer/mni/lib MNI_DIR=/opt/freesurfer/mni MNI_DATAPATH=/opt/freesurfer/mni/data

2024-04-23 21:59:01 UTC (buildkit.dockerfile.v0)

ENV MNI_PERL5LIB=/opt/freesurfer/mni/lib/perl5/5.8.5 PERL5LIB=/opt/freesurfer/mni/lib/perl5/5.8.5 SUBJECTS_DIR=/opt/freesurfer/subjects PATH=/opt/freesurfer/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/opt/fsl/lib:/opt/fsl/bin:/opt/c3d/bin:/usr/lib/afni/bin:/usr/local/miniconda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

2024-04-23 21:59:01 UTC (buildkit.dockerfile.v0)

ENV ANTSPATH=/usr/lib/ants

2024-04-23 21:59:15 UTC (buildkit.dockerfile.v0)

RUN /bin/sh -c mkdir -p $ANTSPATH && curl -sSL "https://dl.dropbox.com/s/gwf51ykkk5bifyj/ants-Linux-centos6_x86_64-v2.3.4.tar.gz" | tar -xzC $ANTSPATH --strip-components 1 # buildkit

2024-04-23 21:59:15 UTC (buildkit.dockerfile.v0)

ENV PATH=/usr/lib/ants:/opt/freesurfer/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/opt/fsl/lib:/opt/fsl/bin:/opt/c3d/bin:/usr/lib/afni/bin:/usr/local/miniconda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

2024-04-23 21:59:17 UTC (buildkit.dockerfile.v0)

RUN /bin/sh -c npm install -g svgo # buildkit

2024-04-23 21:59:28 UTC (buildkit.dockerfile.v0)

RUN /bin/sh -c npm install -g bids-validator@1.8.4 # buildkit

2024-04-23 21:59:28 UTC (buildkit.dockerfile.v0)

ENV MKL_NUM_THREADS=1 OMP_NUM_THREADS=1

2024-04-23 21:59:29 UTC (buildkit.dockerfile.v0)

RUN /bin/sh -c useradd -m -s /bin/bash -G users xcp_d # buildkit

2024-04-23 21:59:29 UTC (buildkit.dockerfile.v0)

WORKDIR /home/xcp_d

2024-04-23 21:59:29 UTC (buildkit.dockerfile.v0)

ENV HOME=/home/xcp_d

2024-04-23 21:59:30 UTC (buildkit.dockerfile.v0)

RUN /bin/sh -c python -c "from matplotlib import font_manager" && sed -i 's/\(backend *: \).*$/\1Agg/g' $( python -c "import matplotlib; print(matplotlib.matplotlib_fname())" ) # buildkit

2024-04-23 21:59:40 UTC (buildkit.dockerfile.v0)

RUN /bin/sh -c python -c "from templateflow import api as tfapi; tfapi.get('MNI152NLin2009cAsym', resolution=2, suffix='T1w', desc=None); tfapi.get(template='MNI152NLin6Asym', resolution=2, suffix='T1w'); tfapi.get('MNI152NLin2009cAsym', resolution=1, desc='carpet',suffix='dseg'); tfapi.get(template='MNI152NLin2009cAsym', mode='image', suffix='xfm', extension='.h5'); tfapi.get('fsLR', density='32k');" && find $HOME/.cache/templateflow -type d -exec chmod go=u {} + && find $HOME/.cache/templateflow -type f -exec chmod go=u {} + # buildkit

2024-04-23 21:59:42 UTC (buildkit.dockerfile.v0)

RUN /bin/sh -c 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" && dpkg -i pandoc-2.2.2.1-1-amd64.deb && rm pandoc-2.2.2.1-1-amd64.deb # buildkit

2024-04-23 21:59:44 UTC (buildkit.dockerfile.v0)

RUN /bin/sh -c find $HOME -type d -exec chmod go=u {} + && find $HOME -type f -exec chmod go=u {} + && rm -rf $HOME/.npm $HOME/.conda $HOME/.empty # buildkit

2024-04-23 21:59:44 UTC (buildkit.dockerfile.v0)

RUN /bin/sh -c ldconfig # buildkit

2024-04-23 21:59:44 UTC (buildkit.dockerfile.v0)

WORKDIR /tmp/

2024-08-16 18:56:36 UTC

/bin/sh -c #(nop) COPY dir:35ce07df08decdfb5e79af0ecee56caa5b7e35a64c47932c499c506604a7cca9 in /src/xcp_d

2024-08-16 18:56:36 UTC

/bin/sh -c #(nop) ARG VERSION=0.0.1

2024-08-16 18:57:41 UTC

|1 VERSION=0.8.1 /bin/sh -c echo "${VERSION}" > /src/xcp_d/xcp_d/VERSION && echo "include xcp_d/VERSION" >> /src/xcp_d/MANIFEST.in && pip install --no-cache-dir "/src/xcp_d[all]"

2024-08-16 18:57:45 UTC

|1 VERSION=0.8.1 /bin/sh -c find $HOME -type d -exec chmod go=u {} + && find $HOME -type f -exec chmod go=u {} + && rm -rf $HOME/.npm $HOME/.conda $HOME/.empty

2024-08-16 18:57:46 UTC

|1 VERSION=0.8.1 /bin/sh -c ldconfig

2024-08-16 18:57:46 UTC

/bin/sh -c #(nop) WORKDIR /tmp/

2024-08-16 18:57:47 UTC

/bin/sh -c #(nop) ENTRYPOINT ["/usr/local/miniconda/bin/xcp_d"]

2024-08-16 18:57:47 UTC

/bin/sh -c #(nop) ARG BUILD_DATE

2024-08-16 18:57:47 UTC

/bin/sh -c #(nop) ARG VCS_REF

2024-08-16 18:57:47 UTC

/bin/sh -c #(nop) ARG VERSION

2024-08-16 18:57:47 UTC

/bin/sh -c #(nop) LABEL org.label-schema.build-date=2024-08-16T18:56:26Z org.label-schema.name=xcp_d org.label-schema.description=xcp_d- postprocessing of fmriprep outputs org.label-schema.url=https://xcp-d.readthedocs.io/ org.label-schema.vcs-ref=7a8f9ba org.label-schema.vcs-url=https://github.com/PennLINC/xcp_d org.label-schema.version=0.8.1 org.label-schema.schema-version=1.0

Danger Zone
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Please be careful as this will not just delete the reference but also the actual content!

For example when you have latest and v1.2.3 both pointing to the same image
the deletion of latest will also permanently remove v1.2.3.

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