99% python fMRI processing setup

02 Aug 2019

Despite a desire to participate in developing open-source software and develop good open science practices, my PhD has involved a lot of proprietary and closed datasets and software due to who I was working with. This summer I have been returning to some fMRI data that I collected ages ago but haven’t gotten around to analyzing due to other projects. Here I want to summarize my experience trying to adopt some better open-science practices and using new tools and standards. I’m coming to this as a relatively seasoned python programmer and data analyzer but having never used these specific tools. I hope this could be useful for someone starting from scratch or someone interested in a newcomer’s experience with these tools.

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Commentary on Brette

14 Mar 2019

I recently responded to the open call for commentary on Romain Brette’s article “Is coding a relevant metaphor for the brain?”, to be published in Behavioral and Brain Sciences. Philosopher Corey Maley and I submitted the following proposal. However, we were not invited to submit our commentary. Here is the brief synopsis of what we had planned to comment on:

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NeurIPS 2018

01 Dec 2018

I’ll present a poster at the NeurIPS 2018 workshop on Interpretability and Robustness in Audio, Speech and Language. Check out our short paper “How transferable are features in convolutional neural network acoustic models across languages?”.

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Presenting at CCN about theories of explanation in neuro and AI

05 Sep 2018

Tomorrow I will be presenting a poster at the Cognitive Computational Neuroscience (CCN) conference entitled “Towards a theory of explanation for biological and artificial intelligence”. Here is the poster along with the short paper that goes with it, as well as some slides that I used in a previous presentation.

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Towards a common philosophy of explanation in AI and neuroscience. Part I

04 Apr 2018

Part I: Integration of deep learning and neuroscience

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Custom workstation build

20 Mar 2017

Last weekend I built a computer. This machine was designed as a workstation for my research, considering the resources needed for the analysis and modelling of large 7T fMRI data and the training/testing of deep neural networks. I used PCPartPicker to help me test out different configurations and check for compatibility issues. Here is the parts list:

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Experience, perception, and physicality in experimental music: An argument for the role of neuroscience in music phenomenology

17 Sep 2016

Alphabet Soup

Maryanne Amacher, composer and installation artist (1938–2009)

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Introduction to Alphabet Soup series

11 Sep 2016

Alphabet Soup

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How many permutations should you perform?

10 Aug 2016

Non-parametric permutation tests or randomization tests are often recommended because they require fewer assumptions of the data. In the recent paper by Eklund et al. non-parametric permutation testing was the only method that consistently gave false positive rates in the expected range.

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Review: A Practical Guide for Improving Transparency and Reproducibility in Neuroimaging Research

28 Jul 2016

Fig 1. Three pillars of Open Science: data, code, and papers. Three pillars of Open Science: data, code, and papers.

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First post

27 Jul 2016

I’ve wanted to make a new blog/website using github pages for a while now. I like the idea of hosting everything on github for free and the simplicity yet flexibility of Jekyll. We considered it briefly when we were deciding what to use for the new Women in Machine Learning website but ended up going with wordpress instead, which was almost definitely the right choice in retrospect and I’m happy with how that website is shaping up. But for my own page, wordpress seemed like overkill and I much prefer to have access to all the moving parts :grin:

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