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update OASIS-TRT individual brains and labels
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‎install/Dockerfile

Lines changed: 16 additions & 10 deletions
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@@ -1,5 +1,5 @@
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# Generated by Neurodocker version 0.4.1
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# Timestamp: 2018-10-05 14:45:31 UTC
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# Generated by Neurodocker version 0.4.2
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# Timestamp: 2018-11-06 01:58:12 UTC
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#
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# Thank you for using Neurodocker. If you discover any issues
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# or ways to improve this software, please submit an issue or
@@ -135,7 +135,7 @@ RUN export PATH="/opt/miniconda-latest/bin:$PATH" \
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nose \
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&& sync && conda clean -tipsy && sync \
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&& bash -c "source activate mb \
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&& pip install --no-cache-dir \
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&& pip install --no-cache-dir \
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datalad[full] \
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duecredit" \
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&& rm -rf ~/.cache/pip/* \
@@ -148,13 +148,19 @@ RUN mkdir -p /opt/data && cd /opt/data && \
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curl -sSL https://osf.io/download/rh9km/?revision=2 -o templates.zip && \
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unzip templates.zip && \
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rm -f /opt/data/templates.zip && \
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curl -sSL https://files.osf.io/v1/resources/hvc52/providers/osfstorage/57c1a8f06c613b01f98d68a9/?zip= -o OASIS-TRT-20_brains.zip && \
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mkdir OASIS-TRT-20_brains && \
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cd OASIS-TRT-20_brains && \
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unzip ../OASIS-TRT-20_brains.zip && \
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cd .. && \
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rm OASIS-TRT-20_brains.zip && \
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curl -sSL https://files.osf.io/v1/resources/zevma/providers/osfstorage/5783dfcab83f6901f963735c/?zip= -o cmalabels.zip && \
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mkdir OASIS-TRT-20_DKT31_CMA_labels_v2 && \
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cd OASIS-TRT-20_DKT31_CMA_labels_v2 && \
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unzip ../cmalabels.zip && \
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cd .. && \
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rm cmalabels.zip && \
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curl -sSL https://osf.io/download/d2cmy/ -o OASIS-TRT-20_jointfusion_DKT31_CMA_labels_in_OASIS-30_v2.nii.gz && \
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curl -sSL https://osf.io/download/qz3kx/ -o OASIS-TRT_brains_to_OASIS_Atropos_template.tar.gz && \
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tar zxf OASIS-TRT_brains_to_OASIS_Atropos_template.tar.gz && \
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rm OASIS-TRT_brains_to_OASIS_Atropos_template.tar.gz && \
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curl -sSL https://osf.io/download/dcf94/ -o OASIS-TRT_labels_to_OASIS_Atropos_template.tar.gz && \
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tar zxf OASIS-TRT_labels_to_OASIS_Atropos_template.tar.gz && \
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rm OASIS-TRT_labels_to_OASIS_Atropos_template.tar.gz && \
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rm -rf __MACOSX
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RUN bash -c 'source /opt/miniconda-latest/etc/profile.d/conda.sh && \
@@ -262,7 +268,7 @@ RUN echo '{ \
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\n ], \
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\n [ \
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\n "run", \
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\n "mkdir -p /opt/data && cd /opt/data && \\\\n curl -sSL https://osf.io/download/rh9km/?revision=2 -o templates.zip && \\\\n unzip templates.zip && \\\\n rm -f /opt/data/templates.zip && \\\\n curl -sSL https://osf.io/download/d2cmy/ -o OASIS-TRT-20_jointfusion_DKT31_CMA_labels_in_OASIS-30_v2.nii.gz && \\\\n curl -sSL https://osf.io/download/qz3kx/ -o OASIS-TRT_brains_to_OASIS_Atropos_template.tar.gz && \\\\n tar zxf OASIS-TRT_brains_to_OASIS_Atropos_template.tar.gz && \\\\n rm OASIS-TRT_brains_to_OASIS_Atropos_template.tar.gz && \\\\n curl -sSL https://osf.io/download/dcf94/ -o OASIS-TRT_labels_to_OASIS_Atropos_template.tar.gz && \\\\n tar zxf OASIS-TRT_labels_to_OASIS_Atropos_template.tar.gz && \\\\n rm OASIS-TRT_labels_to_OASIS_Atropos_template.tar.gz && \\\\n rm -rf __MACOSX" \
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\n "mkdir -p /opt/data && cd /opt/data && \\\\n curl -sSL https://osf.io/download/rh9km/?revision=2 -o templates.zip && \\\\n unzip templates.zip && \\\\n rm -f /opt/data/templates.zip && \\\\n curl -sSL https://files.osf.io/v1/resources/hvc52/providers/osfstorage/57c1a8f06c613b01f98d68a9/?zip= -o OASIS-TRT-20_brains.zip && \\\\n mkdir OASIS-TRT-20_brains && \\\\n cd OASIS-TRT-20_brains && \\\\n unzip ../OASIS-TRT-20_brains.zip && \\\\n cd .. && \\\\n rm OASIS-TRT-20_brains.zip && \\\\n curl -sSL https://files.osf.io/v1/resources/zevma/providers/osfstorage/5783dfcab83f6901f963735c/?zip= -o cmalabels.zip && \\\\n mkdir OASIS-TRT-20_DKT31_CMA_labels_v2 && \\\\n cd OASIS-TRT-20_DKT31_CMA_labels_v2 && \\\\n unzip ../cmalabels.zip && \\\\n cd .. && \\\\n rm cmalabels.zip && \\\\n curl -sSL https://osf.io/download/d2cmy/ -o OASIS-TRT-20_jointfusion_DKT31_CMA_labels_in_OASIS-30_v2.nii.gz && \\\\n rm -rf __MACOSX" \
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\n ], \
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\n [ \
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\n "run_bash", \

‎install/neurodocker.sh

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###############################################################################
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# Generate a dockerfile for building a mindboggle container
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docker run --rm kaczmarj/neurodocker:0.4.1 generate docker \
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docker run --rm kaczmarj/neurodocker:0.4.2 generate docker \
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--base neurodebian:stretch \
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--pkg-manager apt \
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--install graphviz tree git-annex-standalone vim \
@@ -64,13 +64,19 @@ docker run --rm kaczmarj/neurodocker:0.4.1 generate docker \
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curl -sSL https://osf.io/download/rh9km/?revision=2 -o templates.zip && \
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unzip templates.zip && \
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rm -f /opt/data/templates.zip && \
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curl -sSL https://files.osf.io/v1/resources/hvc52/providers/osfstorage/57c1a8f06c613b01f98d68a9/?zip= -o OASIS-TRT-20_brains.zip && \
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mkdir OASIS-TRT-20_brains && \
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cd OASIS-TRT-20_brains && \
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unzip ../OASIS-TRT-20_brains.zip && \
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cd .. && \
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rm OASIS-TRT-20_brains.zip && \
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curl -sSL https://files.osf.io/v1/resources/zevma/providers/osfstorage/5783dfcab83f6901f963735c/?zip= -o cmalabels.zip && \
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mkdir OASIS-TRT-20_DKT31_CMA_labels_v2 && \
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cd OASIS-TRT-20_DKT31_CMA_labels_v2 && \
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unzip ../cmalabels.zip && \
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cd .. && \
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rm cmalabels.zip && \
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curl -sSL https://osf.io/download/d2cmy/ -o OASIS-TRT-20_jointfusion_DKT31_CMA_labels_in_OASIS-30_v2.nii.gz && \
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curl -sSL https://osf.io/download/qz3kx/ -o OASIS-TRT_brains_to_OASIS_Atropos_template.tar.gz && \
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tar zxf OASIS-TRT_brains_to_OASIS_Atropos_template.tar.gz && \
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rm OASIS-TRT_brains_to_OASIS_Atropos_template.tar.gz && \
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curl -sSL https://osf.io/download/dcf94/ -o OASIS-TRT_labels_to_OASIS_Atropos_template.tar.gz && \
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tar zxf OASIS-TRT_labels_to_OASIS_Atropos_template.tar.gz && \
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rm OASIS-TRT_labels_to_OASIS_Atropos_template.tar.gz && \
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rm -rf __MACOSX' \
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--run-bash 'source /opt/miniconda-latest/etc/profile.d/conda.sh && \
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conda activate mb && \

‎mindboggle/mindboggle123

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@@ -300,9 +300,9 @@ if args.skip_ants:
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else:
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comps = TDIR.split(os.sep)
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IDIR = os.sep.join(comps[:(-2 if not comps[-1] else -1)] +
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['OASIS-TRT_brains_to_OASIS_Atropos_template'])
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['OASIS-TRT-20_brains'])
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LDIR = os.sep.join(comps[:(-2 if not comps[-1] else -1)] +
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['OASIS-TRT_labels_to_OASIS_Atropos_template'])
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['OASIS-TRT-20_DKT31_CMA_labels_v2'])
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T1s = human_order_sorted(glob(os.path.join(IDIR, '*.nii.gz')))
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labels = human_order_sorted(glob(os.path.join(LDIR, '*.nii.gz')))
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N = args.segN or len(T1s)

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