[DATALAD] Added subdataset

.gitmodules

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+	datalad-url = git@github.com:aswendtlab/AIDAmri.git

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code/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib64/
+parts/
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+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
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+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/

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code/ARA/AllenBrainAPI-master/README.md

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+# README #
+
+Tools for accessing the Allen Atlas API from MATLAB. 
+e.g. downloading images, projection data, searching for particular experiments, etc. 
+Functionality isn't complete right now and is a bit rough in places, but everything works and the functions should provide a good template for showing you how to add functionality. 
+For more details see the [Allen API documentation](http://help.brain-map.org/display/mouseconnectivity/API). 
+You will need to install [JSONlab](http://ch.mathworks.com/matlabcentral/fileexchange/33381-jsonlab--a-toolbox-to-encode-decode-json-files-in-matlab-octave) for some functions to work. 
+
+
+
+### Examples ###
+
+Get structure list that underlies the Allen Reference Atlas:
+```
+>> S=getAllenStructureList;
+```
+
+
+Keep only the areas that are children of `Cerebellum`:
+```
+>> S=getAllenStructureList('childrenOf','Cerebellum');
+```
+
+### Also see ###
+There are other useful functions too. See:
+
+* DownloadImageSeries.m 
+* findAllenExperiments.m
+* getInjectionIDfromExperiment.m
+* getProjectionDataFromExperiment.m

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code/README.md

@@ -1,3 +1,77 @@
-All custom code goes into this directory. All scripts should be written such
-that they can be executed from the root of the dataset, and are only using
-relative paths for portability.
+[1.2]: http://i.imgur.com/wWzX9uB.png
+[1]: http://www.twitter.com/AswendtMarkus
+<!--social icon from https://github.com/carlsednaoui/gitsocial -->
+
+<img align="left" src="https://github.com/maswendt/AIDAmri/blob/master/AIDA_Logo.png" width="120">
+<h1>AIDA<i>mri</i></h1>
+
+Atlas-based Imaging Data Analysis Pipeline (AIDA) for structural and functional MRI of the mouse brain
+<br/>
+<br/>
+<h3><b>Manual v1.1</h3></b>
+
+[**Link**](https://github.com/maswendt/AIDA/blob/master/manual.pdf)
+
+[<h3><b>DOCKER (PRE-RELEASE)</h3></b>](https://github.com/aswendtlab/AIDAmri/tree/dockerdev)
+Check out the dockerdev branch to use our Dockerfile to easily build the pipeline. A separate manual can be accessed [here](https://github.com/aswendtlab/AIDAmri/blob/dockerdev/Docker_manual.pdf).
+
+
+<h3><b>EXAMPLE FILES</h3></b>
+
+Download [**here**](https://doid.gin.g-node.org/70e11fe472242e2d4f96c53ac9b0a556/). 
+Mouse MRI data, acquired with Bruker 9.4T - cryo coil setup: adult C57BL7/6 mouse, 
+T2-weighted (anatomical scan),
+DTI (structural connectivty scan),
+rs-fMRI (functional connectivity scan).
+
+[<h3><b>ARA CREATOR</h3></b>](https://github.com/maswendt/AIDAmri/ARA)
+Matlab script to generate a custom version of the Allen Mouse Brain Atlas.
+
+<h3><b>VERSION HISTORY</h3></b>
+
+[Information about Version 1.1.1 (Docker pre-release)](https://github.com/maswendt/AIDAmri/releases/tag/1.1.1)
+<br/>
+[Information about Version 1.1 (Stable)](https://github.com/maswendt/AIDAmri/releases/tag/v1.1)
+<br/>
+[Information about Version 1.0](https://github.com/maswendt/AIDAmri/releases/tag/v1.0)
+
+[<h3><b>CONTACT</h3></b>](https://neurologie.uk-koeln.de/forschung/ag-neuroimaging-neuroengineering/)
+Markus Aswendt (markus.aswendt@uk-koeln.de)[![alt text][1.2]][1]
+
+Need help? Chat with us and find answers to FAQs in the AIDA_Tools Gitter room: [![Gitter](https://badges.gitter.im/AIDA_tools/community.svg)](https://gitter.im/AIDA_tools/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge)
+
+<h3><b>LICENSE/CITATION</h3></b>
+GNU General Public License v3.0
+<br/>
+<br/>
+If you use our software or modify parts of it and use it in other ways, please cite: 
+<br/>
+<br/>
+
+*Pallast N, Diedenhofen M, Blaschke S, Wieters F, Wiedermann D, Hoehn M, Fink GR, Aswendt M. Processing Pipeline for Atlas-Based Imaging Data Analysis of Structural and Functional Mouse Brain MRI (AIDAmri). Front Neuroinform. 2019 Jun 4;13:42.[doi: 10.3389/fninf.2019.00042.](https://doi.org/10.3389/fninf.2019.00042)*
+___
+<details>
+<summary>REFERENCES</summary></b>
+
++ Brain Connectivity Toolbox
+    + [M. Rubinov and O. Sporns (2010). Complex Network Measures of Brain Connectivity: Uses 
+and Interpretations. NeuroImage 52 (3), 1059–69.](https://www.sciencedirect.com/science/article/abs/pii/S105381190901074X)
++ Allen Mouse Brain Reference Atlas
+    + [Wang et al. (2020). The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas. Cell 181 (4), 936-953.](https://pubmed.ncbi.nlm.nih.gov/32386544/)
++ Niftyreg
+    + [Ourselin, et al. (2001). Reconstructing a 3D structure from serial
+histological sections. Image and Vision Computing, 19(1-2), 25–31.](https://www.sciencedirect.com/science/article/pii/S0262885600000524)
+    + [Modat, et al. (2014). Global image registration using a symmetric block-
+matching approach. Journal of Medical Imaging, 1(2), 024003–024003.](https://www.ncbi.nlm.nih.gov/pubmed/26158035)
+    + [Rueckert, et al.. (1999). Nonrigid registration using free-form
+deformations: Application to breast MR images. IEEE Transactions on Medical
+Imaging, 18(8), 712–721.](https://ieeexplore.ieee.org/document/796284)
+    + [Modat, et al. (2010). Fast free-form deformation using graphics processing
+units. Computer Methods And Programs In Biomedicine,98(3), 278–284.](https://www.ncbi.nlm.nih.gov/pubmed/19818524)
++ FSL
+    + [M.W. Woolrich, S. Jbabdi, B. Patenaude, M. Chappell, S. Makni, T. Behrens, C. Beckmann, M. Jenkinson, S.M. Smith. Bayesian analysis of neuroimaging data in FSL. NeuroImage, 45:S173-86, 2009](https://www.ncbi.nlm.nih.gov/pubmed/19059349)
+    + [S.M. Smith, M. Jenkinson, M.W. Woolrich, C.F. Beckmann, T.E.J. Behrens, H. Johansen-Berg, P.R. Bannister, M. De Luca, I. Drobnjak, D.E. Flitney, R. Niazy, J. Saunders, J. Vickers, Y. Zhang, N. De Stefano, J.M. Brady, and P.M. Matthews. Advances in functional and structural MR image analysis and implementation as FSL. NeuroImage, 23(S1):208-19, 2004](https://www.sciencedirect.com/science/article/pii/S1053811904003933?via%3Dihub)
+    + [M. Jenkinson, C.F. Beckmann, T.E. Behrens, M.W. Woolrich, S.M. Smith. FSL. NeuroImage, 62:782-90, 2012](https://www.sciencedirect.com/science/article/pii/S1053811911010603?via%3Dihub) 
++ DSIstudio
+    + [Yeh, Fang-Cheng, et al. Deterministic diffusion fiber tracking improved by quantitative anisotropy. (2013): e80713. PLoS ONE 8(11)](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0080713)
+</details>

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