Hallo,
These are the IPython notebooks and slides about model-based fMRI analysis part of the Summer School on Model Based Neuroscience 2015 in Amsterdam, hosted by the Birte Forstmann research group.
- You can find all the notebooks in "notebooks"-folder. You can download them to your own computer.
- To install Python, IPython, IPython notebook and all the necessary libraries, have a look at Anaconda.
- You can download my slides here.
Here you can find some nice resources on how to use Python in cognitive neuroscience: http://bender.astro.sunysb.edu/classes/python-science/
You can also view the notebooks in nbviewer. You won't be able to change the code, but it can still be instructive:
- Part 1: Preprocessing fMRI data with Nipype (answers)
- Part 2: Analyzing behavioral data and fitting a hierarhical DDM in Python (answers)
- Part 3: Analyzing behavioral data and fitting a hierarhical DDM in Python (answers)
- Part 4: Extract fMRI signal from ROI (answers)
- Part 5: fit GLM and use as input to HDDM (answers)
To do the practicals yourself you will need the data of Leendert van Maanens 2011 Journal of Neuroscience-paper. We are working on publishing this data for free, right now you can email me at gilles.de.hollander@gmail.com for the data.
Cheers,
Gilles de Hollander
June 2015