diff --git a/README.md b/README.md index 35c8c73..5b9d39e 100644 --- a/README.md +++ b/README.md @@ -1,13 +1,13 @@ Spatial frequency preferences ============================== -[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/billbrod/spatial-frequency-preferences/HEAD?filepath=notebooks) +[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/billbrod/spatial-frequency-preferences/v1.0.0?filepath=notebooks) An fMRI experiment to determine the relationship between spatial frequency and eccentricity in the human early visual cortex. -See the paper **LINK** for scientific details. If you re-use some component -of this project in an academic publication, see the [citing](#citation) section -for how to credit us. +See the [paper](https://doi.org/10.1101/2021.09.27.462032) for scientific +details. If you re-use some component of this project in an academic +publication, see the [citing](#citation) section for how to credit us. # Usage @@ -75,7 +75,7 @@ We also include several jupyter notebooks in the `notebooks/` directory: approximations thereof. If you'd like to use them, you can either view it on -[Binder](https://mybinder.org/v2/gh/billbrod/spatial-frequency-preferences/HEAD?filepath=notebooks) +[Binder](https://mybinder.org/v2/gh/billbrod/spatial-frequency-preferences/v1.0.0?filepath=notebooks) or [install jupyter](https://jupyterlab.readthedocs.io/en/stable/getting_started/installation.html) so you can view it locally (you can also view a static version of the notebooks @@ -244,6 +244,10 @@ simplify things: I don't like how I handle `DATA_DIR` right now and am working on simplifying it, but that's what we have for now. +This image only contains the python environment. Therefore, it only can run the +steps of the analysis after `GLMdenoise` (i.e., from `partially-processed` or +`fully-processed`, not from `preprocessed`). + ### Experimental environment We also include a separate environment containing psychopy, if you wish to run @@ -284,7 +288,7 @@ use-case: happens because we're running a fake snakemake run to make sure that the timestamps are correct, so it doesn't try to rerun the preprocessing steps. -2. `partially-processed`: Partially-processed data is shared on OSF (**LINK**). +2. `partially-processed`: Partially-processed data will be shared shortly. If you want to re-run our 1d tuning curve analysis and the 2d model fits, this is the one you should use. It is not fully BIDS-compliant, but tries to be BIDS-inspired. -- this is currently under development @@ -741,7 +745,8 @@ the fit the model, though it does contain the loss function we used, # Citation If you use the data or code (including the stimuli) from this project in an -academic publication, please cite the paper (**LINK**). Additionally: +academic publication, please cite the +[paper](https://doi.org/10.1101/2021.09.27.462032). Additionally: 1. If you use the code in this or any of the linked repos [above](#related-repos) directly (for example, using it to generate the log-polar stimuli, modifying that code to create a similar set of stimuli,