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-
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-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
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-# Installer logs
-pip-log.txt
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-
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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

@@ -1,77 +0,0 @@
-[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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