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Merge pull request miykael#50 from djarecka/datalad_oldver
fix/workaround for issues with new releases of datalad, matplotlib, pybids/grabbit
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‎Dockerfile

Lines changed: 10 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -1,11 +1,11 @@
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# Generated by Neurodocker v0.3.2-7-g4b0f32d.
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# Generated by Neurodocker v0.3.2.
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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
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# pull request on our GitHub repository:
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# https://github.com/kaczmarj/neurodocker
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#
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# Timestamp: 2018-02-26 18:15:43
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# Timestamp: 2018-03-07 15:33:37
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FROM neurodebian:stretch-non-free
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@@ -108,7 +108,7 @@ RUN conda create -y -q --name neuro python=3.6 \
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jupyter_contrib_nbextensions \
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traits \
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pandas \
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matplotlib \
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matplotlib=2.1.2 \
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scikit-learn \
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seaborn \
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nbformat \
@@ -117,7 +117,7 @@ RUN conda create -y -q --name neuro python=3.6 \
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&& pip install -q --no-cache-dir https://github.com/nipy/nipype/tarball/master \
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https://github.com/INCF/pybids/tarball/master \
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nilearn \
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datalad[full] \
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datalad[full]==0.9.1 \
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nipy \
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duecredit" \
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&& sync \
@@ -140,8 +140,7 @@ RUN mkdir /output && chmod 777 /output && chmod a+s /output
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USER neuro
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# User-defined BASH instruction
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RUN bash -c "source activate neuro && cd /data && datalad install -r ///workshops/nih-2017/ds000114 \
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&& cd /data/ds000114 && datalad get -r -J4 sub-*/ses-test/anat && datalad get -r -J4 sub-*/ses-test/func/*fingerfootlips* && datalad get -r -J4 derivatives/fmriprep/sub-*/anat/*space-mni152nlin2009casym_preproc.nii.gz && datalad get -r -J4 derivatives/fmriprep/sub-*/anat/*t1w_preproc.nii.gz && datalad get -r -J4 derivatives/fmriprep/sub-*/anat/*h5 && datalad get -r -J4 derivatives/freesurfer/sub-01"
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RUN bash -c "source activate neuro && cd /data && datalad install -r ///workshops/nih-2017/ds000114 && cd ds000114 && paths=\"///workshops/nih-2017/ds000114 && cd ds000114 && datalad get -r -J4 sub-*/ses-test/anat sub-*/ses-test/func/*fingerfootlips* derivatives/fmriprep/sub-*/anat/*space-mni152nlin2009casym_preproc.nii.gz derivatives/fmriprep/sub-*/anat/*t1w_preproc.nii.gz derivatives/fmriprep/sub-*/anat/*h5 derivatives/freesurfer/sub-01\" && datalad --report-status=failure get -r -J4 \"$paths\" || datalad --report-status=failure get -r \"$paths\""
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# User-defined BASH instruction
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RUN bash -c "curl -L https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/580705089ad5a101f17944a9 -o /data/ds000114/derivatives/fmriprep/mni_icbm152_nlin_asym_09c.tar.gz && tar xf /data/ds000114/derivatives/fmriprep/mni_icbm152_nlin_asym_09c.tar.gz -C /data/ds000114/derivatives/fmriprep/. && rm /data/ds000114/derivatives/fmriprep/mni_icbm152_nlin_asym_09c.tar.gz"
@@ -211,8 +210,8 @@ RUN echo '{ \
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\n "miniconda", \
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\n { \
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\n "miniconda_version": "4.3.31", \
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\n "conda_install": "python=3.6 pytest jupyter jupyterlab jupyter_contrib_nbextensions traits pandas matplotlib scikit-learn seaborn nbformat", \
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\n "pip_install": "https://github.com/nipy/nipype/tarball/master https://github.com/INCF/pybids/tarball/master nilearn datalad[full] nipy duecredit", \
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\n "conda_install": "python=3.6 pytest jupyter jupyterlab jupyter_contrib_nbextensions traits pandas matplotlib=2.1.2 scikit-learn seaborn nbformat", \
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\n "pip_install": "https://github.com/nipy/nipype/tarball/master https://github.com/INCF/pybids/tarball/master nilearn datalad[full]==0.9.1 nipy duecredit", \
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\n "env_name": "neuro", \
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\n "activate": true \
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\n } \
@@ -243,7 +242,7 @@ RUN echo '{ \
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\n ], \
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\n [ \
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\n "run_bash", \
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\n "source activate neuro && cd\t/data && datalad install -r ///workshops/nih-2017/ds000114\\n&& cd /data/ds000114 && datalad get -r -J4 sub-*/ses-test/anat && datalad get -r -J4 sub-*/ses-test/func/*fingerfootlips* && datalad get -r -J4 derivatives/fmriprep/sub-*/anat/*space-mni152nlin2009casym_preproc.nii.gz && datalad get -r -J4 derivatives/fmriprep/sub-*/anat/*t1w_preproc.nii.gz && datalad get -r -J4 derivatives/fmriprep/sub-*/anat/*h5 && datalad get -r -J4 derivatives/freesurfer/sub-01" \
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\n "source activate neuro && cd\t/data && datalad install -r ///workshops/nih-2017/ds000114 && cd ds000114 && paths=\"///workshops/nih-2017/ds000114 && cd ds000114 && datalad get -r -J4 sub-*/ses-test/anat sub-*/ses-test/func/*fingerfootlips* derivatives/fmriprep/sub-*/anat/*space-mni152nlin2009casym_preproc.nii.gz derivatives/fmriprep/sub-*/anat/*t1w_preproc.nii.gz derivatives/fmriprep/sub-*/anat/*h5 derivatives/freesurfer/sub-01\" && datalad --report-status=failure get -r -J4 \"$paths\" || datalad --report-status=failure get -r \"$paths\"" \
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\n ], \
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\n [ \
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\n "run_bash", \
@@ -279,6 +278,6 @@ RUN echo '{ \
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\n ] \
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\n ] \
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\n ], \
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\n "generation_timestamp": "2018-02-26 18:15:43", \
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\n "neurodocker_version": "0.3.2-7-g4b0f32d" \
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\n "generation_timestamp": "2018-03-07 15:33:37", \
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\n "neurodocker_version": "0.3.2" \
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\n}' > /neurodocker/neurodocker_specs.json

‎create_dockerfile.sh

Lines changed: 3 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -9,10 +9,10 @@ docker run --rm kaczmarj/neurodocker:master generate -b neurodebian:stretch-non-
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--user=neuro \
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--miniconda miniconda_version="4.3.31" \
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conda_install="python=3.6 pytest jupyter jupyterlab jupyter_contrib_nbextensions
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traits pandas matplotlib scikit-learn seaborn nbformat" \
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traits pandas matplotlib=2.1.2 scikit-learn seaborn nbformat" \
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pip_install="https://github.com/nipy/nipype/tarball/master
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https://github.com/INCF/pybids/tarball/master
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nilearn datalad[full] nipy duecredit" \
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nilearn datalad[full]==0.9.1 nipy duecredit" \
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env_name="neuro" \
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activate=True \
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--run-bash "source activate neuro && jupyter nbextension enable exercise2/main && jupyter nbextension enable spellchecker/main" \
@@ -21,8 +21,7 @@ docker run --rm kaczmarj/neurodocker:master generate -b neurodebian:stretch-non-
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--run 'mkdir /data && chmod 777 /data && chmod a+s /data' \
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--run 'mkdir /output && chmod 777 /output && chmod a+s /output' \
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--user=neuro \
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--run-bash 'source activate neuro && cd /data && datalad install -r ///workshops/nih-2017/ds000114
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&& cd /data/ds000114 && datalad get -r -J4 sub-*/ses-test/anat && datalad get -r -J4 sub-*/ses-test/func/*fingerfootlips* && datalad get -r -J4 derivatives/fmriprep/sub-*/anat/*space-mni152nlin2009casym_preproc.nii.gz && datalad get -r -J4 derivatives/fmriprep/sub-*/anat/*t1w_preproc.nii.gz && datalad get -r -J4 derivatives/fmriprep/sub-*/anat/*h5 && datalad get -r -J4 derivatives/freesurfer/sub-01' \
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--run-bash 'source activate neuro && cd /data && datalad install -r ///workshops/nih-2017/ds000114 && cd ds000114 && paths="///workshops/nih-2017/ds000114 && cd ds000114 && datalad get -r -J4 sub-*/ses-test/anat sub-*/ses-test/func/*fingerfootlips* derivatives/fmriprep/sub-*/anat/*space-mni152nlin2009casym_preproc.nii.gz derivatives/fmriprep/sub-*/anat/*t1w_preproc.nii.gz derivatives/fmriprep/sub-*/anat/*h5 derivatives/freesurfer/sub-01" && datalad --report-status=failure get -r -J4 "$paths" || datalad --report-status=failure get -r "$paths"' \
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--run-bash 'curl -L https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/580705089ad5a101f17944a9 -o /data/ds000114/derivatives/fmriprep/mni_icbm152_nlin_asym_09c.tar.gz && tar xf /data/ds000114/derivatives/fmriprep/mni_icbm152_nlin_asym_09c.tar.gz -C /data/ds000114/derivatives/fmriprep/. && rm /data/ds000114/derivatives/fmriprep/mni_icbm152_nlin_asym_09c.tar.gz' \
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--copy . "/home/neuro/nipype_tutorial" \
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--user=root \

‎notebooks/basic_data_input_bids.ipynb

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@@ -156,7 +156,7 @@
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"metadata": {},
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"outputs": [],
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"source": [
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"[f.filename for f in layout.get(subject='01', type='bold', extensions=['nii', 'nii.gz'])]"
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"layout.get(subject='01', type='bold', extensions=['nii', 'nii.gz'], return_type='file')"
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]
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},
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{
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" \n",
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" layout = BIDSLayout(data_dir)\n",
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" \n",
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" bolds = [f.filename for f in layout.get(subject=subject_id, type=\"bold\", extensions=['nii', 'nii.gz'])]\n",
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" bolds = layout.get(subject=subject_id, type=\"bold\", return_type='file', extensions=['nii', 'nii.gz'])\n",
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" \n",
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" return bolds"
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]
@@ -325,7 +325,7 @@
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" \n",
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" layout = BIDSLayout(data_dir)\n",
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" \n",
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" T1w = [f.filename for f in layout.get(subject=subject_id, modality=\"anat\")]\n",
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" T1w = layout.get(subject=subject_id, modality=\"anat\", return_type='file')\n",
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" \n",
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" return T1w\n",
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"\n",
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" \n",
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" layout = BIDSLayout(data_dir)\n",
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" \n",
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" bolds = [f.filename for f in layout.get(subject=subject_id, type=\"bold\", \n",
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" extensions=['nii', 'nii.gz'])]\n",
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" bolds = layout.get(subject=subject_id, type=\"bold\", return_type='file', extensions=['nii', 'nii.gz'])\n",
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" \n",
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" return bolds\n",
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"\n",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.6.3"
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"version": "3.6.4"
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}
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},
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"nbformat": 4,

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