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Shuo Han
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Merge remote-tracking branch 'upstream/master' into shuo_fixed_colors
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‎.gitignore

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/docs/_build
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doctrees
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mindboggle.*.box
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mindboggle.egg-info
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vtk_cpp_tools/bin
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.vagrant/
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build
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CMakeCache.txt

‎README.rst

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‎THANKS.rst

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Thanks
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==============================================================================
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| Mindboggle is an open source project for brain image analysis using Python.
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| It is a community project with a growing list of contributors (see `people <http://mindboggle.info/people.html>`_).
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| Below is a list of software contributors in chronological order.
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Mindboggle is an open source project for brain image analysis using Python.
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+-------------------------+-------------------------------------+-------------------------------------------+
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| | | |
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+-------------------------+-------------------------------------+-------------------------------------------+
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| **Contributors** | **Contact** | **Primary contributions** |
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+-------------------------+-------------------------------------+-------------------------------------------+
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| `Arno Klein`_ | [email protected] | Main developer |
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+-------------------------+-------------------------------------+-------------------------------------------+
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| `Forrest Bao`_ | forrest.bao [at] gmail.com | VTK i/o, spectra port [1], MST fundi |
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+-------------------------+-------------------------------------+-------------------------------------------+
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| Joachim Giard | joachimgiard [at] gmail.com | C++ surface shapes (depth, curvature) |
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+-------------------------+-------------------------------------+-------------------------------------------+
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| Yrjo Hame | yrjo.hame [at] gmail.com | HMMF fundi |
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+-------------------------+-------------------------------------+-------------------------------------------+
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| Eliezer Stavsky | eli.stavsky [at] gmail.com | Label propagation |
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+-------------------------+-------------------------------------+-------------------------------------------+
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| Elias Chaibub Neto | elias.chaibub.neto [at] sagebase.org| Statistical analysis (R code) |
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+-------------------------+-------------------------------------+-------------------------------------------+
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| Daniel Clark | daniel.clark [at] childmind.org | Install script (bash) |
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| | | |
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+-------------------------+-------------------------------------+-------------------------------------------+
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| **Tank Think Labs** | | |
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| `Satrajit Ghosh`_ | satra [at] mit.edu | Nipype and informatics help |
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| `Nolan Nichols`_ | nolan.nichols [at] gmail.com | Linked data i/o |
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+-------------------------+-------------------------------------+-------------------------------------------+
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| Brian Rossa | brian.rossa [at] gmail.com | Zernike moments port [2] |
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| Oliver Hinds | ohinds [at] gmail.com | Label propagation |
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| | | |
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| **Third party** | | |
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| `Martin Reuter`_ | mreuter [at] nmr.mgh.harvard.edu | [1] Laplace-Beltrami spectra (Matlab) |
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+-------------------------+-------------------------------------+-------------------------------------------+
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| Arthur Mikhno | arthur.mikhno [at] gmail.com | [2] Zernike moments (Matlab) |
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+-------------------------+-------------------------------------+-------------------------------------------+
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| Hal Canary | hal [at] cs.unc.edu | vtkviewer_ (Python VTK viewer) |
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+-------------------------+-------------------------------------+-------------------------------------------+
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| | | |
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+-------------------------+-------------------------------------+-------------------------------------------+
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It is a community project with a growing number of contributors.
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.. _`Arno Klein`: http://binarybottle.com
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.. _`Satrajit Ghosh`: http://mit.edu/~satra
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.. _`Forrest Bao`: https://sites.google.com/site/forrestbao/
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.. _`Nolan Nichols`: http://www.linkedin.com/in/nolannichols
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.. _`Martin Reuter`: http://reuter.mit.edu/
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.. _vtkviewer: https://github.com/HalCanary/vtkviewer
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Please see `people <http://mindboggle.info/people.html>`_ for an updated list.

‎docs/faq.rst

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faq/why_mindboggle
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faq/why_license
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faq/why_python
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faq/citing_mindboggle
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faq/run_time
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labels
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faq/singularity

‎docs/faq/citing_mindboggle.rst

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.. _citing_mindboggle:
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------------------------------------------------------------------------------
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How do we cite Mindboggle?
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------------------------------------------------------------------------------
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For Mindboggle-related articles, visit `mindboggle.info/papers.html <http://mindboggle.info/papers.html>`_.
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When using Mindboggle please cite the primary reference:
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A Klein, SS Ghosh, FS Bao, J Giard, Y Hame, E Stavsky, N Lee, B Rossa, M Reuter, EC Neto, A Keshavan. 2017.
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**Mindboggling morphometry of human brains**.
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*PLoS Computational Biology* 13(3): e1005350. `doi:10.1371/journal.pcbi.1005350 <http://dx.doi.org/10.1371/journal.pcbi.1005350>`_
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Contributors are listed on Mindboggle's `team page <http://mindboggle.info/people.html>`_.
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‎docs/faq/run_time.rst

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without Laplace-Beltrami spectra or Zernike moments,
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Mindboggle took less than 7 minutes using the following command::
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mindboggle $FREESURFER_SUBJECT --working $MINDBOGGLING \
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--out $MINDBOGGLED --no_volumes --no_sulci --no_moments --no_spectra
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mindboggle $FREESURFER_SUBJECT --out $MINDBOGGLED \
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--no_volumes --no_sulci --no_moments --no_spectra

‎docs/faq/singularity.rst

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.. _singularity:
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------------------------------------------------------------------------------
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How do I create and use a Singularity image rather than Docker?
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------------------------------------------------------------------------------
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To convert the Mindboggle Docker image to a Singularity image, run::
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singularity pull mindboggle.img docker://nipy/mindboggle
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After the conversion, you'll need 3 mounts (data, working directory, and
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home directory) for it to work. Here is an example of the full command
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together with some of the optional arguments (thanks, Satra!), using the same
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environment variables as in the `README <http://mindboggle.info/software.html>`_::
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singularity run \
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-B $HOST:$DOCK:ro \
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-B $PWD:$DOCK \
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-B $PWD/jovyan:/home/jovyan \
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-e mindboggle.img \
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$DOCK/example_mri_data/T1.nii.gz \
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--id arno \
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--fs_T2image $DOCK/example_mri_data/T2.nii.gz \
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--plugin MultiProc --plugin_args "dict(n_procs=2)" \
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--fs_openmp 5 --ants_num_threads 5 --mb_num_threads 10
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‎docs/faq/why_mindboggle.rst

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- wrote docstring tests for almost every function
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- set up continuous testing on circleci.com (tests are run every time a commit is made to the GitHub repository)
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Please see our updated Mindboggle `team page <http://mindboggle.info/people.html>`_.
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‎docs/images/mindboggle_logo_200px_600dpi.jpg

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