Charestlab / nsddatapaper_rsa

rsa analyses for the data paper

nsddatapaper_rsa

rsa analyses for the data paper

this is a set of scripts that will process nsd fmri data, mask in a set of regions of interest along the ventral stream, compute representational dissimilarity matrices from all pairs condition activity patterns, and finally plot the TSNE two-dimensional solutions for those RDMs.

to install simply clone this repo, cd to it's directory and

python setupy.py develop

this will install the package and all other required packages.

additionally, you may need to install Tomas Knapen's nsd_access

pip install git+https://github.com/tknapen/nsd_access.git

nsd_access is a convenient tool for quickly and easily accessing data from the Natural Scenes Dataset. For more details and tutorials see the repo here: https://github.com/tknapen/nsd_access

It might be worth familiarising yourself with the Natural Scenes Dataset before you begin too. You can do so with the NSD Data Manual

first, you need to compute the category labels with

python nsd_prepare_category_labels.py

second, you need to prepare the masked betas in rois along the ventral stream with

python nsd_prepare_rois_rdms.py 0

this will prepare RDMs for all the ROIs for subject 0, which is in fact NSD subj01.

finally, you can plot the TSNE or MDS with

python nsd_plot_tsne.py 0

this will create a series of plots from the paper, for subj01.