Indexing for the CNL github
**Table of Contents **
To find all the code we put online, we need some sort of overview. We have this by looking at this index. However this index only works if we all keep it up-to-date together. Plus once you make a change, you will be part of the contributors, so people can see that you worked on this. Showing that we do this all together.
Anyone that adds a repo to the CNL page. It doesn't matter if you created it or if you only forked it. If you put it in the main CNL GitHub, you need to add to this index. If you do not do this, it might get deleted after a while to prevent us loosing track of what is what.
As soon as you add anything to the main CNL GitHub.
create a new branch by clicking on the "main button" and typing a name for your new branch and clicking the create branch option.
Let's say you are the first to create the subgroup "pipelines". You look below the line that says "## index" and look alphabetically where it goes. Since it's a subgroup, you put 2 # before the name + 1 space. After that you need to add this also to the table of content. You do this by scrolling up to the table of content, look where your subgroup goes and add it there by writing the title as is in between [] directly followed by the title without capitals and spaces/underscores replaced by - in-between (). Make sure there is the same amount of indents as for the other sub-groups.
Find the right subgroup and lets say in this case you want to upload your pipeline. Look for "### pipelines", and see where your pipeline goes alphabetically. add 4 # before the name of your repo. Then enter the name of your repo between []followed by the URL inside (). In the line below write a quick explanation with at least the following info, year when uploaded, who created the Fork, what language you used, references if they exist. You can add more, but try to keep it as short as possible, since every repo should have a readme that explains itself. After that you need to add this also to the table of content. You do this by scrolling up to the table of content, look for your subgroup and add it below there (alphabetically) by writing the title as is in between [] directly followed by the title without capitals and spaces/underscores replaced by - in-between (). Make sure there is the same amount of indents as for the other repos.
After saving all the changes you made in the new branch. Click on the "pull requests button". Click the green "New pull request" button. Make sure you are comparing the right branches with each other. This means the "main" branch should be the first box and whatever you called yours should be in the one on the right. After that you hit "create pull request" two times. If correct you can now choose "merge pull request". After this you should delete your old branch.
The index is divided in sub-groups. If your repo does not fall within a subgroup, feel free to create a new one.
2022 - Laura Ziemer, Douwe Horsthuis, Kamy Wakim - EEG data collection protocol
2018 - Olga Sysoeva - Presentation paradigm - - created and used for Olga and Tufikameni's Rett project
2022 - Douwe Horsthuis - presentation paradigm - created and used for SFARI project (2021)
???? - Lab Paradigm - Presentation paradigm - published on mulitple times
2014 - Lab Paradigm - Presentation paradigm - Adaptation of Beep-flash-kids (2014) Used orignally for Murphy paper
2020 - Douwe Horsthuis - Presentation paradigm - created and used for Ana Francisco's 22q and schizophrenia research to measure active and passive inhibition.
2022 - Douwe Horsthuis - Presentation Paradigm - created and used for SFARI project (2021)
2021 - Douwe Horsthuis - Presentation paradigm - created and used for Ana Francisco's cystinosis project (2021)
2021 - Emily Knight - Presentation paradigm - creatd and used for specific ASD study, modified for Sfari project
2021 - Douwe Horsthuis - Presentation Paradigm - Created and used for Ana Francisco's Cystinosis Project (2021)
2021 - Douwe Horsthuis - Presentation Paradigm - visual Duration discrimination - created and used for Ana Francisco's cystinosis project (2021)
2021 - Douwe Horsthuis - Presentation Paradigm - Visual Oddball - created but not used for Ana Francisco's cystinosis project (2021)
2021 - Luke Shaw - presentation Paradigm - Oddball duration tone - created and used for several lab studies - updated with extra soas by Douwe
2020 - Douwe Horsthuis - Presentation Paradigm - Duration discrimination - created and used for Ana Francisco's 22q/schizophrenia cystinosis project (2021)
2020 - Douwe Horsthuis - Presentation Paradigm - Omission - created and used for Ana Francisco's 22q/schizophrenia project (2020)
2020 - Douwe Horsthuis - Presentation Paradigm - Rhythm - created and used for Ana Francisco's 22q/schizophrenia (2021)
???? - Filip De Sanctis - Presentation Paradigm - Optical flow paradigm with go-no-go task for MoBI
2022 - Douwe Horsthuis - Presentation Paradigm - Simple restingstate paradigm with eyetracking for SFARI project (2021)
2021 - Douwe Horsthuis - Presentation Paradigm - updated the swat_kids paradigm (2021) original used for Wylie Javitt Foxe
2021- Douwe Horsthuis - Presentation paradigm - created for Ana Francisco's Cystinosis project (2021)
2021 - Shlomit Beker - Matlab - Anticipatory analysis of data from ASD children (aka VAMP)
- Beker, S., Foxe, J. J., Molholm S., (https://www.biorxiv.org/content/10.1101/2020.05.07.083154v1)
2022 - Douwe Horsthuis - Matlab - EEG pipeline to pre-process data and get a report of the quality of the data.(Behavioral, Eye tracking, Time frequency, ERPS)
2021 - Douwe Horsthuis - Matlab and R - EEG pipeline relying on EEGlab/ERPlab and potential for statistics (including mixed effect models) in R studio
- Francisco, A. A., Foxe, J. J., Horsthuis, D. J., DeMaio, D., & Molholm, S. (2020). Assessing auditory processing endophenotypes associated with Schizophrenia in individuals with 22q11. 2 deletion syndrome. Translational psychiatry, 10(1), 1-11
- Francisco, A. A., Horsthuis, D. J., Popiel, M., Foxe, J. J., & Molholm, S. (2020). Atypical response inhibition and error processing in 22q11. 2 Deletion Syndrome and schizophrenia: Towards neuromarkers of disease progression and risk. NeuroImage: Clinical, 27, 102351.
- Francisco, A. A., Foxe, J. J., Horsthuis, D. J., & Molholm, S. (2020). Impaired auditory sensory memory in Cystinosis despite typical sensory processing: A high-density electrical mapping study of the mismatch negativity (MMN). NeuroImage: Clinical, 25, 102170.
- Francisco, A. A., Berruti, A. S., Kaskel, F. J., Foxe, J. J., & Molholm, S. (2021). Assessing the integrity of auditory processing and sensory memory in adults with cystinosis (CTNS gene mutations). Orphanet Journal of Rare Diseases, 16(1), 1-10.
2021 - Ana Francisco, Douwe Horsthuis, Filip De Sanctis - Matlab - Pipeline to analyse Resting state data using EEGlab, looking at microstates and power/frequency
2022 - Douwe Horsthuis, Shlomit Beker, Filip De Sanctis, Sophie Molholm - Pipeline to analyse all Sfari projects, mostly frequency domain related
2021 - General lab effort - Matlab SPSS - Pipeline to pre-process SiN data
2021 - Shlomit Beker - Matlab - Test-retest
- Beker, S. Foxe, J.J., Venticinque, J. et al., Journal of Neurodevelopmental Disorders (2021)
2021- Shlomit Beker - Matlab - FDR (false discovery rate)
2021- Ana Francisco - R - Mixed effect models - Single trial data.
2021- Shlomit Beker - Matlab - Rett Standard ITPC
2021 - (forked) SCCN/UCSD - Matlab - EEGLAB is an open source signal processing environment for electrophysiological signals running on Matlab and developed at the SCCN/UCSD
2021- (forked) Donders institute -Matlab - The MATLAB toolbox for MEG, EEG and iEEG analysis
2019- (forked) LIMO Team - Hierarchical Linear Modelling for MEEG data
2020- (forked) Mick cross - Matlab - A MATLAB Package for Relating Neural Signals to Continuous Stimuli
2021 - Douwe Horsthuis - Presentation - Presentation code that is needed to add eye tracking to your paradigm, double checked by the people from SR-research.
2022- Douwe Horsthuis - Matlab - function to plot what channels got deleted on idividual level or how often on group level
2022 - Douwe Horsthuis - Matlab - Matlab code to plot directly into a powerpoint instead of having to input figures manually into it.
2021 - Ana Francisco, Douwe Horsthuis, Filip De Sanctis, Sophie Molholm and Seyda Tikir - Matlab - A script for practicing what components to delete after doing ICA using EEGlab and its IClabel toolbox to verify.
2021 - Douwe Horsthuis - Matlab - function that transforms your 160 channel data into 64, leaving the landmark channels alone.
2019 - (forked)othneildrew - HTML/Markdown - Readme template for Github
2021 - Douwe Horsthuis - Matlab - to export data from EEGlab to external programs keeping individual trials.
These repos are currently in use to work in colaboration on projects. Most will be set to private. This means that you cannot google them, you cannot see/find them unless you are a part of this github organization.
Distributed under the MIT License. See LICENSE for more information.
Cognitive Neurophysiology Lab - @CNL_Einstein - cnl@einsteinmed.org - cogneurolabrochester@gmail.com
https://www.cognitiveneurolab.com/
https://www.urmc.rochester.edu/labs/cognitive-neurophysiology.aspx
