The past week I have been busy preparing my lectures and practical for the model-based summer school 2017. It was great fun to meet these students and I have learned a lot myself, setting up the practical. Rather than using a dataset of Birte’s lab, this year I used three datasets from openfmri.org, which are already in the BIDS-format. This makes it very easy to use open source tools like fmriprep.
I was very impressed how easy it now is to run very sophisticated preprocessing workflows, using a plethora of neuroimaging software packages and libraries, using the virtual machine approach of Docker and Singularity. On the LISA cluster it was a bit more challenging. Because Singularity automatically mounts your $HOME directory, the packages installed in the container then starts looking for dotfiles (.local/lib/python) it should not use. A solution is to (temprorally) rename your .local-folder, or use something like this, where we overwrite an environment variable (PYTHONUSERBASE) in the virtual environment:
SINGULARITYENV_PYTHONUSERBASE=<some_bogus_folder> singularity run -B /run/shm/:/run/shm/ -e poldracklab_fmriprep_latest-2017-07-20-11e274f76dc3.img /home/gholland/data/bistable /home/gholland/data/bistable/derivatives participant --participant-label 01
The next thing that was really cool to look into is traditional massively univariate analyses in Python using nistats, a derivative of nilearn, developed in Paris and Berkeley.
Anyway, to see how to do an entire model-based neuroimaging-analysis in just a few dozen lines of code, have a look at the notebooks I prepared for the summer school here:
On SFN Neuroscience 2015 in Chicago I presented two posters.
One was about optimizing 7T fMRI in the basal ganglia during the stop signal task, the other one about modelling the HRF as to link its shape not computational cognitive models.
I’m delighted that our paper on the problems of disentangling the BOLD signals from the subtantia nigra and subthalamic nucleus has been published online.
You can find it here (pdf).
(Also mentioned in a Tweet by NeuroSkeptic: “Subversive”!)
My paper with EJ Wagenmakers, Lourens Waldorp and Birte Forstmann on the ‘in limbo approach’ has been accepted in PLOS ONE. You can download the latest version here.
I implemented a little wrapper for fast-dm which makes it easier to use fast-dm in a python environment. You can fide the code on github
. There is also an IPython notebook
. that shows how to use it.
Last week I presented my poster “An antidote to the imager’s fallacy, or how to identify brain areas that are in limbo” at the Organization for Human Brain Mapping conference in Hamburg. A wonderful week with many inspiring talks and meetings. You can download my poster here.
My paper on an iron gradient in the Subthalamic Nucleus has been published in Human Brain Mapping.
de Hollander, G., Keuken, M. C., Bazin, P.-L., Weiss, M., Neumann, J., Reimann, K., Wähnert, M., Turner, R., Forstmann, B. U. and Schäfer, A. (2014), A gradual increase of iron toward the medial-inferior tip of the subthalamic nucleus. Hum. Brain Mapp.. doi: 10.1002/hbm.22485 (pdf)
I gave a workshop on using Python for data analysis in Cognitive Neuroscience.
You can find the slides here and a corresponding IPython notebook here.
I will give the talk about the In Limbo project this afternoon (11 november 2013), San Diego time, 14:15 at meeting room 7B. You can find the slides here.
Code can be found here.