pRF fitting workshop

This is the repo for the pRF fitting workshop, to be held on Dec 5 in Amsterdam. The notebook containing the entire workshop is located next to this README, and can be run on our notebook server at the VU (but only on the day of the workshop).

If you just want to view the notebook on GitHub, go here: PRF_demo.ipynb

You'll need to login to brainimaging.labs.vu.nl, with password and username as described below. Then, open up a new terminal (right top, drop-down menu), and type: git clone https://github.com/tknapen/prf_fitting_workshop.git. Once this has downloaded today's materials, you can close the terminal browser tab, and open the PRF_demo.ipynb notebook in the folder prf_fitting_workshop.

List of students

Your login is the student_XX string in front of your name in the table below.

login	First and last name
student_00	Marlene Roesner
student_01	Jelle van Dijk
student_02	Jonathan van Leeuwen
student_03	Evert Boonstra
student_04	Luisa Prochazkova
student_05	Kiki Arkesteijn
student_06	Laura - Isabelle Klatt
student_07	Andromachi Tsouli
student_08	katya olmos
student_09	Anne Trutti
student_10	Roel van Dooren
student_11	Eduard Ort
student_12	Roderik Gerritsen
student_13	Ingmar de Vries
student_14	Isabell Meier
student_15	Daniel Lindh
student_16	Remo van der Heiden
student_17	Iris Schutte
student_18	Ya Gao
student_19	Mengsi Xu
student_20	Aisu Li
student_21	Kayla Stone
student_22	Elle van Heusden
student_23	Dana van Son
student_24	Yang Liu
student_25	Martijn van Ackooij
student_26	Franca Parianen
student_27	Gijs Holleman
student_28	Nicolas Carvajal Sanchez
student_29	Bauke van der Velde
student_30	Marcelo Malbec
student_31	Ibrahim Hakami

How to use at home

If you want to run this workshop's materials at home, you will have to install the necessary software. This is a working python environment and, inside it, a set of python packages. Here's a brief step-by-step guide.

• First, download the conda installer from the webpage explaining how to install conda: anaconda.com. We recommend you use miniconda, as this is the most frugal option in terms of disk usage. If you have a Mac or Linux computer, you'll likely end up downloading some .sh file. I don't know how this works for Windows. I'm sure this is not the first time you hear that serious scientific software is not available for Windows.
• Install conda. This can often be done by entering something like bash miniconda_version_installer.sh (depending on the file you downloaded) and answering the relevant questions
• Create your first environment: conda create -n prf_workshop python=3.6
• From now on, this environment can be 'activated' by: conda activate prf_workshop (or, for older conda versions: source activate prf_workshop). Please activate your environment.
• You'll have to install a bunch of packages.
  • conda install -c conda-forge jupyter numpy matplotlib scipy pandas seaborn cython nibabel nilearn
  • remaining packages are installed with pip:
  • pip install sharedmem popeye
• You're done. You can now start a notebook server somewhat like the one you worked on in the workshop on your own computer (preferably in this folder) by: jupyter notebook

Note that your system will have to have some things installed for this to work; ffmpeg is necessary for the movies of the experimental design, and you will need a compiler to be able to install popeye.