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Update gh-pages - 2017-07-31 13:26:32
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‎index.html

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</p><p>
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All of the notebooks used in this tutorial can be found on <a href="https://github.com/djarecka/nipype_tutorial">github.com/djarecka/nipype_tutorial</a>.
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For the tutorial, we will use a Docker container. You need to install a <a href="http://www.docker.com/">Docker</a> and download a docker image that provides you a
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neuroimaging environment based on a Debian system, with working Python 3 software (including Nipype, dipy, matplotlib,
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nibabel, nipy, numpy, pandas, scipy, seaborn and more), FSL, AFNI, ANTs and SPM12 (no license needed).
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TODO
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neuroimaging environment based on a Debian system, with working Python 3 software (including Nipype, matplotlib,
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nibabel, numpy, pandas, scipy, and more), FSL, AFNI, ANTs and SPM12 (no license needed).
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</p><p>
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For everything that isn't covered in this tutorial, check out the <a href="http://nipype.readthedocs.io/en/latest/">main homepage</a>.
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</p>

‎notebooks/basic_data_input.html

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<h1 id="Dataset-structure">Dataset structure<a class="anchor-link" href="#Dataset-structure">&#182;</a></h1><p>To be able to import data, you first need to be aware about the structure of your dataset. The structure of the dataset for this tutorial is according to BIDS, and looks as follows:</p>
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<pre><code>ds000114
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├── CHANGES
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├── dataset_description.json
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├── derivatives
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│ ├── fmriprep
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│ │ └── sub01...sub10
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│ │ └── ...
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│ ├── freesurfer
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│ │ └── ...
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│ ├── fsaverage
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│ ├── fsaverage5
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│ │ └── sub01...sub10
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│ │ └── ...
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├── dwi.bval
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├── dwi.bvec
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├── sub-01
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│ ├── anat
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│ │ └── sub-01_T1w.nii.gz
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│ └── func
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│ ├── sub-01_task-fingerfootlips_bold.nii.gz
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│ ├── sub-01_task-linebisection_bold.nii.gz
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│ └── sub-01_task-linebisection_events.tsv
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│ └── dwi
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│ └── sub-01_dwi.nii.gz
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├── sub-02
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│ ├── anat
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│ │ └── sub-02_T1w.nii.gz
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│ └── func
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│ ├── sub-02_task-fingerfootlips_bold.nii.gz
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│ ├── sub-02_task-linebisection_bold.nii.gz
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│ └── sub-02_task-linebisection_events.tsv
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│ └── dwi
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│ └── sub-02_dwi.nii.gz
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│ ├── ses-retest
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│ ├── anat
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│ │ └── sub-01_ses-retest_T1w.nii.gz
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│ ├──func
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│ ├── sub-01_ses-retest_task-covertverbgeneration_bold.nii.gz
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│ ├── sub-01_ses-retest_task-fingerfootlips_bold.nii.gz
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│ ├── sub-01_ses-retest_task-linebisection_bold.nii.gz
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│ ├── sub-01_ses-retest_task-linebisection_events.tsv
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│ ├── sub-01_ses-retest_task-overtverbgeneration_bold.nii.gz
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│ └── sub-01_ses-retest_task-overtwordrepetition_bold.nii.gz
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│ └── dwi
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│ └── sub-01_ses-retest_dwi.nii.gz
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│ ├── ses-test
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│ ├── anat
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│ │ └── sub-01_ses-test_T1w.nii.gz
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│ ├──func
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│ ├── sub-01_ses-test_task-covertverbgeneration_bold.nii.gz
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│ ├── sub-01_ses-test_task-fingerfootlips_bold.nii.gz
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│ ├── sub-01_ses-test_task-linebisection_bold.nii.gz
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│ ├── sub-01_ses-test_task-linebisection_events.tsv
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│ ├── sub-01_ses-test_task-overtverbgeneration_bold.nii.gz
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│ └── sub-01_ses-test_task-overtwordrepetition_bold.nii.gz
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│ └── dwi
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│ └── sub-01_ses-retest_dwi.nii.gz
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├── sub-02..sub-10
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│ └── ...
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├── task-covertverbgeneration_bold.json
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├── task-covertverbgeneration_events.tsv
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├── task-fingerfootlips_bold.json
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├── task-fingerfootlips_events.tsv
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└── task-linebisection_bold.json</code></pre>
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├── task-linebisection_bold.json
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├── task-overtverbgeneration_bold.json
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├── task-overtverbgeneration_events.tsv
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├── task-overtwordrepetition_bold.json
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└── task-overtwordrepetition_events.tsv</code></pre>
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