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Merge pull request #14 from gagnonanthony/feat/mcribs
New infant segmentation pipeline. New module to format labels from the Desikan-Killiany atlas. Tissue-specific fodf outputs. Infant surface reconstruction. New docker image for M-CRIB-S and InfantFS.
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| Original file line number | Diff line number | Diff line change |
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| name: fsl | ||
| channels: | ||
| - https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/ | ||
| - conda-forge | ||
| dependencies: | ||
| - python =3.11 | ||
| - mkl=2023.2.0 | ||
| - mkl-service=2.4.0 | ||
| # Base scientific python stack; required by FSL, so pinned here | ||
| - numpy=1.26 | ||
| - scipy=1.11 | ||
| - matplotlib=3.8 | ||
| - pandas=2.2 | ||
| - h5py=3.10 | ||
| - nitime=0.10 | ||
| - scikit-image=0.22 | ||
| - scikit-learn=1.4 | ||
| # FSL dependencies. | ||
| - fsl-bet2=2111.4 | ||
| - fsl-flirt=2111.2 | ||
| - fsl-fast4=2111.3 | ||
| - fsl-fugue=2201.4 | ||
| - fsl-mcflirt=2111.0 | ||
| - fsl-miscmaths=2203.2 | ||
| - fsl-topup=2203.2 |
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| ARG BASE_IMAGE=ubuntu:jammy-20240405 | ||
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| # Older Python to support legacy MCRIBS (taken from nibabies Dockerfile) | ||
| FROM python:3.6.15-slim AS pyenv | ||
| RUN pip install --no-cache-dir numpy nibabel scipy pandas numexpr contextlib2 imageio \ | ||
| && cp /usr/lib/x86_64-linux-gnu/libffi.so.7* /usr/local/lib | ||
|
|
||
| # Download FSL. | ||
| FROM ${BASE_IMAGE} AS build-fsl | ||
|
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| RUN apt-get update && \ | ||
| apt-get install -y --no-install-recommends \ | ||
| build-essential \ | ||
| binutils \ | ||
| bzip2 \ | ||
| ca-certificates \ | ||
| curl \ | ||
| unzip \ | ||
| && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* | ||
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| WORKDIR / | ||
| RUN echo "2024.04.25" && curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj | ||
| ENV MAMBA_ROOT_PREFIX="/opt/conda" | ||
|
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||
| # Fetch the FSL environment | ||
| COPY fsl.yml fsl.yml | ||
| RUN micromamba create -y -f fsl.yml && \ | ||
| micromamba clean --all --yes | ||
| ENV PATH="/opt/conda/envs/fsl/bin:$PATH" | ||
|
|
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| # Set a stage for the build | ||
| FROM ${BASE_IMAGE} AS runtime | ||
|
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| ENV DEBIAN_FRONTEND="noninteractive" \ | ||
| LANG="en_US.UTF-8" \ | ||
| LC_ALL="en_US.UTF-8" | ||
|
|
||
| RUN apt-get update && \ | ||
| apt-get install -y --no-install-recommends \ | ||
| apt-utils \ | ||
| bc \ | ||
| build-essential \ | ||
| ca-certificates \ | ||
| curl \ | ||
| git \ | ||
| gnupg \ | ||
| libtool \ | ||
| locales \ | ||
| lsb-release \ | ||
| tcsh \ | ||
| netbase \ | ||
| unzip \ | ||
| xvfb \ | ||
| # MCRIBS-required | ||
| libboost-dev \ | ||
| libeigen3-dev \ | ||
| libflann-dev \ | ||
| libgl1-mesa-dev \ | ||
| libglu1-mesa-dev \ | ||
| libssl-dev \ | ||
| libxt-dev \ | ||
| zlib1g-dev && \ | ||
| locale-gen en_US.UTF-8 && \ | ||
| apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* | ||
|
|
||
| # Configure PPAs for libpng12 and libxp6 | ||
| RUN GNUPGHOME=/tmp gpg --keyserver hkps://keyserver.ubuntu.com --no-default-keyring --keyring /usr/share/keyrings/linuxuprising.gpg --recv 0xEA8CACC073C3DB2A \ | ||
| && GNUPGHOME=/tmp gpg --keyserver hkps://keyserver.ubuntu.com --no-default-keyring --keyring /usr/share/keyrings/zeehio.gpg --recv 0xA1301338A3A48C4A \ | ||
| && echo "deb [signed-by=/usr/share/keyrings/linuxuprising.gpg] https://ppa.launchpadcontent.net/linuxuprising/libpng12/ubuntu jammy main" > /etc/apt/sources.list.d/linuxuprising.list \ | ||
| && echo "deb [signed-by=/usr/share/keyrings/zeehio.gpg] https://ppa.launchpadcontent.net/zeehio/libxp/ubuntu jammy main" > /etc/apt/sources.list.d/zeehio.list | ||
|
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||
| # Install ANTs | ||
| COPY --from=gagnonanthony/ants@sha256:0abd03bc59c10ea4a93e399d07c5e4019cf8eb89963a54e050f209ed73722dce /opt/ants /opt/ants | ||
| ENV PATH="/opt/ants/bin:$PATH" \ | ||
| ANTSPATH="/opt/ants" \ | ||
| LD_LIBRARY_PATH="/opt/ants/lib:$LD_LIBRARY_PATH" | ||
|
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| # Install FreeSurfer (with Infant Module) | ||
| COPY --from=nipreps/freesurfer@sha256:3b895fc732a7080374a15c4f976510f39c0c48dc76c030ab27316febd5e419ee /opt/freesurfer /opt/freesurfer | ||
| ENV FREESURFER_HOME="/opt/freesurfer" | ||
| ENV SUBJECTS_DIR="$FREESURFER_HOME/subjects" \ | ||
| FUNCTIONALS_DIR="$FREESURFER_HOME/sessions" \ | ||
| MNI_DIR="$FREESURFER_HOME/mni" \ | ||
| LOCAL_DIR="$FREESURFER_HOME/local" \ | ||
| MINC_BIN_DIR="$FREESURFER_HOME/mni/bin" \ | ||
| MINC_LIB_DIR="$FREESURFER_HOME/mni/lib" \ | ||
| MNI_DATAPATH="$FREESURFER_HOME/mni/data" \ | ||
| FSL_DIR=${FSLDIR} \ | ||
| FREESURFER="/opt/freesurfer" | ||
| ENV PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \ | ||
| MNI_PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \ | ||
| PATH="$FREESURFER_HOME/bin:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH" | ||
|
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| # Install MCRIBS from nipreps (with legacy Python) | ||
| COPY --from=gagnonanthony/mcribs@sha256:12ddd74a0d47f055bea4bb19cc0df5b39d0b3ee2aa76d4276d4bfea6f169b2b5 /opt/MCRIBS/ /opt/MCRIBS | ||
| COPY --from=pyenv /usr/local/lib/ /usr/local/lib/ | ||
| COPY --from=pyenv /usr/local/bin/python3 /opt/MCRIBS/bin/python | ||
| ENV PATH="/opt/MCRIBS/bin:/opt/MCRIBS/MIRTK/MIRTK-install/bin:/opt/MCRIBS/MIRTK/MIRTK-install/lib/tools:${PATH}" \ | ||
| LD_LIBRARY_PATH="/opt/MCRIBS/lib:/opt/MCRIBS/ITK/ITK-install/lib:/opt/MCRIBS/VTK/VTK-install/lib:/opt/MCRIBS/MIRTK/MIRTK-install/lib:/usr/local/lib:${LD_LIBRARY_PATH}" \ | ||
| MCRIBS_HOME="/opt/MCRIBS" \ | ||
| PYTHONPATH="/opt/MCRIBS/lib/python:/usr/local/lib/python3.6/site-packages/:${PYTHONPATH}" | ||
|
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||
| # Install FSL | ||
| COPY --from=build-fsl /bin/micromamba /bin/micromamba | ||
| COPY --from=build-fsl /opt/conda/envs/fsl /opt/conda/envs/fsl | ||
| ENV MAMBA_ROOT_PREFIX="/opt/conda" \ | ||
| PATH="${PATH}:/opt/conda/envs/fsl/bin" \ | ||
| CPATH="/opt/conda/envs/fsl/include:${CPATH}" \ | ||
| LD_LIBRARY_PATH="/opt/conda/envs/fsl/lib:${LD_LIBRARY_PATH}" \ | ||
| CONDA_PYTHON="/opt/conda/envs/fsl/bin/python" | ||
|
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| # FSL environment. | ||
| ENV LANG="C.UTF-8" \ | ||
| LC_ALL="C.UTF-8" \ | ||
| PYTHONNOUSERSITE=1 \ | ||
| FSLDIR="/opt/conda/envs/fsl" \ | ||
| FSLOUTPUTTYPE="NIFTI_GZ" \ | ||
| FSLMULTIFILEQUIT="TRUE" \ | ||
| FSLLOCKDIR="" \ | ||
| FSLMACHINELIST="" \ | ||
| FSLREMOTECALL="" \ | ||
| FSLGECUDAQ="cuda.q" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,56 @@ | ||
| #!/bin/python | ||
|
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| import argparse | ||
| import logging | ||
|
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| import pandas as pd | ||
|
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| def _build_arg_parser(): | ||
| p = argparse.ArgumentParser(description=__doc__, | ||
| formatter_class=argparse.RawTextHelpFormatter) | ||
|
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| p.add_argument('-i', '--input', required=True, | ||
| help='Input freesurfer stats file (.stats)') | ||
| p.add_argument('-o', '--output', required=True, | ||
| help='Output tsv file') | ||
|
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| p.add_argument('-m', '--measure', required=True, | ||
| help='Measure to extract from stats file', | ||
| choices=['GrayVol', 'SurfArea', 'ThickAvg']) | ||
| p.add_argument('-s', '--subject', required=True, | ||
| help='Subject ID') | ||
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| return p | ||
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| def main(): | ||
| parser = _build_arg_parser() | ||
| args = parser.parse_args() | ||
| logging.getLogger().setLevel(logging.INFO) | ||
|
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| # Load stats file. | ||
| df = pd.read_csv(args.input) | ||
|
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| # Freesurfer stats file have regions as rows and measures as columns, | ||
| # need to transpose it with the desired measure. | ||
| df_m = df.loc[:, ["StructName", args.measure]].T | ||
|
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| # Setting the first row as the column names. | ||
| df_m.columns = df_m.iloc[0] | ||
|
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| # Dropping the first row. | ||
| df_m = df_m[1:] | ||
|
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| # Replace first column name with "Sample" and add subject ID. | ||
| df_m.columns.name = "Sample" | ||
| df_m.index = [args.subject] | ||
|
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| # Dropping the medial wall column. | ||
| df_m = df_m.drop(columns="Medial_Wall") | ||
|
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| # Save to tsv. | ||
| df_m.to_csv(args.output, sep='\t', index=True, header=True) | ||
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| if __name__ == '__main__': | ||
| main() |
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