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* Add workbench to qsirecon (#6) * Update Dockerfile * Update Dockerfile * update amico * continued * update mamba repo * Install c3d with mamba (#8) * Install c3d and ants with mamba. * Update Dockerfile_Micromamba * Drop ANTS install. * Reformat AtlasPack into a BIDS-Atlas dataset (#7) Reformat AtlasPack into a BIDS-Atlas dataset. * Reorganize QSIRecon atlases into a BIDS-Atlas dataset (#9) * Use new version of QSIRecon atlases. * Change location of AtlasPack. --------- Co-authored-by: Matt Cieslak <[email protected]> Co-authored-by: Taylor Salo <[email protected]>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,62 @@ | ||
| # Copied from: fMRIPrep Docker Container Image distribution | ||
| # | ||
| # MIT License | ||
| # | ||
| # Copyright (c) 2021 The NiPreps Developers | ||
| # | ||
| # Permission is hereby granted, free of charge, to any person obtaining a copy | ||
| # of this software and associated documentation files (the "Software"), to deal | ||
| # in the Software without restriction, including without limitation the rights | ||
| # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | ||
| # copies of the Software, and to permit persons to whom the Software is | ||
| # furnished to do so, subject to the following conditions: | ||
| # | ||
| # The above copyright notice and this permission notice shall be included in all | ||
| # copies or substantial portions of the Software. | ||
| # | ||
| # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | ||
| # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | ||
| # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | ||
| # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | ||
| # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | ||
| # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE | ||
| # SOFTWARE. | ||
|
|
||
| FROM nvidia/cuda:11.2.2-devel-ubuntu18.04 | ||
| ARG TAG_ANTS | ||
|
|
||
| RUN apt-get update && \ | ||
| apt-get install -y --no-install-recommends \ | ||
| ca-certificates \ | ||
| curl \ | ||
| libblas-dev \ | ||
| liblapack-dev \ | ||
| build-essential \ | ||
| libglu1-mesa-dev \ | ||
| bzip2 \ | ||
| libgomp1 \ | ||
| wget | ||
|
|
||
| # Create a shared $HOME directory | ||
| RUN useradd -m -s /bin/bash -G users qsiprep | ||
| WORKDIR /home/qsiprep | ||
| ENV HOME="/home/qsiprep" | ||
|
|
||
| WORKDIR / | ||
| RUN echo "2024.04.11" | ||
| RUN curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba | ||
|
|
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| ENV MAMBA_ROOT_PREFIX="/opt/conda" \ | ||
| MAMBA_NO_LOW_SPEED_LIMIT=1 \ | ||
| PIP_DEFAULT_TIMEOUT=100 | ||
|
|
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| COPY qsirecon_env.yml /tmp/env.yml | ||
|
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| WORKDIR /tmp | ||
| RUN micromamba config set extract_threads 1 | ||
| RUN micromamba create -vv -y -f /tmp/env.yml | ||
| ENV PATH=/opt/conda/envs/qsiprep/bin:$PATH | ||
| RUN micromamba clean -y -a | ||
|
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| RUN mkdir -p ${HOME}/.dipy \ | ||
| && python -c "import amico; amico.core.setup()" |
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| name: qsiprep | ||
| channels: | ||
| - conda-forge | ||
| dependencies: | ||
| - mkl | ||
| - mkl-service | ||
| - numpy=1.23.5 | ||
| - scipy=1.11 | ||
| - fury | ||
| # Workflow dependencies: Convert3d | ||
| - convert3d=1.4 | ||
| # Python dependencies | ||
| - python=3.10 | ||
| - pip | ||
| - pip: | ||
| - bids-validator==1.14.1 | ||
| - coverage | ||
| - dipy==1.8.0 | ||
| - dmri-amico==2.0.3 | ||
| - jinja2==3.0.3 | ||
| - keras==2.8.0 | ||
| - matplotlib==3.8.3 | ||
| - nibabel==5.2.1 | ||
| - nilearn==0.10.1 | ||
| - nipype==1.8.6 | ||
| - niworkflows >=1.9,<= 1.10 | ||
| - numpy==1.23.5 | ||
| - pandas==1.5.3 | ||
| - pillow==10.3.0 | ||
| - pyafq==1.3.2 | ||
| - pytest==8.2.2 | ||
| - pytest-cov==5.0.0 | ||
| - pytest-env==1.1.3 | ||
| - protobuf==3.19.6 | ||
| - scikit-image==0.22.0 | ||
| - scikit-learn==1.4.0 | ||
| - sentry-sdk==1.40.6 | ||
| - simpleitk==2.3.1 | ||
| - sqlalchemy==2.0.27 | ||
| - templateflow==23.1.0 | ||
| - tensorflow-gpu==2.8.4 | ||
| - torch==1.13.1 | ||
| - transforms3d==0.4.1 | ||
| - trx-python==0.2.9 | ||
| - xvfbwrapper==0.2.9 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,59 @@ | ||
| """Convert the AtlasPack folder into a BIDS dataset.""" | ||
|
|
||
| import json | ||
| import os | ||
| import re | ||
| import shutil | ||
|
|
||
| if __name__ == "__main__": | ||
| # Where all the files are located | ||
| in_dir = os.getenv("QSIRECON_ATLASPACK") | ||
|
|
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| with open(os.path.join(in_dir, "dataset_description.json"), "w") as fo: | ||
| json.dump( | ||
| {"Name": "AtlasPack", "BIDSVersion": "1.9.0", "DatasetType": "atlas"}, | ||
| fo, | ||
| ) | ||
|
|
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| # Define patterns and corresponding target formats | ||
| patterns = [ | ||
| (r"atlas-([a-zA-Z0-9+]+)_dseg.tsv", r"atlas-\1/atlas-\1_dseg.tsv"), | ||
| ( | ||
| r"tpl-MNI152NLin6Asym_atlas-([a-zA-Z0-9+]+)_res-01_dseg.nii.gz", | ||
| r"atlas-\1/atlas-\1_space-MNI152NLin6Asym_res-01_dseg.nii.gz", | ||
| ), | ||
| ( | ||
| r"tpl-MNI152NLin2009cAsym_atlas-([a-zA-Z0-9+]+)_res-01_dseg.nii.gz", | ||
| r"atlas-\1/atlas-\1_space-MNI152NLin2009cAsym_res-01_dseg.nii.gz", | ||
| ), | ||
| ( | ||
| r"tpl-fsLR_atlas-([a-zA-Z0-9+]+)_den-91k_dseg.dlabel.nii", | ||
| r"atlas-\1/atlas-\1_space-fsLR_den-91k_dseg.dlabel.nii", | ||
| ), | ||
| ( | ||
| r"tpl-MNI152NLin6Asym_atlas-([a-zA-Z0-9+]+)_dseg.json", | ||
| r"atlas-\1/atlas-\1_space-MNI152NLin6Asym_res-01_dseg.json", | ||
| ), | ||
| ( | ||
| r"tpl-MNI152NLin2009cAsym_atlas-([a-zA-Z0-9+]+)_dseg.json", | ||
| r"atlas-\1/atlas-\1_space-MNI152NLin2009cAsym_res-01_dseg.json", | ||
| ), | ||
| ( | ||
| r"tpl-fsLR_atlas-([a-zA-Z0-9+]+)_dseg.json", | ||
| r"atlas-\1/atlas-\1_space-fsLR_den-91k_dseg.json", | ||
| ), | ||
| ] | ||
|
|
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| for pattern, target_format in patterns: | ||
| files = [f for f in os.listdir(in_dir) if re.search(pattern, f)] | ||
| for filename in files: | ||
| atlas_name = re.findall(pattern, filename)[0] | ||
| target_dir = os.path.join(in_dir, f"atlas-{atlas_name}") | ||
| target_path = os.path.join(in_dir, target_format.replace(r"\1", atlas_name)) | ||
|
|
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| # Create target directory if it doesn't exist | ||
| os.makedirs(target_dir, exist_ok=True) | ||
|
|
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| # Move and rename the file | ||
| shutil.move(os.path.join(in_dir, filename), target_path) | ||
| print(f"Moved {filename} to {target_path}") |
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