spatial_frequency_preferences

# README

This `spatial_frequency_preferences` dataset contains the data from the paper
"Mapping Spatial Frequency Preferences Across Human Primary Visual Cortex", by
William F. Broderick, Eero P. Simoncelli, and Jonathan Winawer, the preprint for
which can be found on
[biorxiv](https://www.biorxiv.org/content/10.1101/2021.09.27.462032).

In this experiment, we measured the BOLD responses of 12 human observers to a
set of novel grating stimuli in order to measure the spatial frequency tuning in
primary visual cortex across eccentricities, retinotopic angles, and stimulus
orientations. We then fit a parametric model which fits all voxels for a given
subject simultaneously, predicting each voxel's response as a function of the
voxel's retinotopic location and the stimulus local spatial frequency and
orientation.

This dataset contains the minimally pre-processed, BIDS-compliant data required
to reproduce the analyses presented in the paper. In addition to the task
imaging data and stimuli files, it contains three `derivatives` directories:

- `freesurfer`: freesurfer subject directories for each subject, with one
change: the contents of `mri/` directories have been defaced.

- `prf_solutions`: solutions to the population receptive field models from a
separate retinotopy experiment for each subject, fit using
[VistaSoft](https://github.com/vistalab/vistasoft). Also contains the Benson
retinotopic atlases for each subject (Benson et al., 2014) and the solutions
for Bayesian retinotopic analyses (Benson and Winawer, 2018) -- the solutions
to the Bayesian retinotopy are what we actually use in the paper.

- `preprocessed`: the preprocessed data (a custom script was used for
preprocessing, found on the [Winawer Lab
Github](https://github.com/WinawerLab/MRI_tools/), see [Winawer Lab
wiki](https://wikis.nyu.edu/pages/viewpage.action?pageId=86054639) for more
details). See paper for description of steps taken. Results should not change
substantially if fMRIPrep were to be used for preprocessing instead, as long
as data is kept in individual subject space.

This dataset is presented with the intention of enabling re-running our analyses
to reproduce our results with our accompanying [Github
repo](https://github.com/billbrod/spatial-frequency-preferences). This dataset
should contain sufficient information for re-analysis with a novel method, but
there are no guarantees.

## Details related to access to the data

Contact person: William F. Broderick, ORCID 0000-0002-8999-9003, [e-mail]

If you use this dataset in a publication, please cite the corresponding paper.

This dataset is hosted on OpenNeuro, and can be downloaded from there.
Additionally, we present two additional variants of this data, see the [Github
README](https://github.com/billbrod/spatial-frequency-preferences) for details
on how to obtain:

- Fully-processed data: contains the final output of our analyses, the data
required to reproduce the figures as they appear in the paper.

- Partially-processed data: contains the outputs of GLMdenoise and all data
required to start fitting the spatial frequency response functions.

The partially-processed data set builds on top of this one and so requires the
data contained here as well, while fully-processed stands alone.

All of the variants may be downloaded using code found in the [Github
repo](https://github.com/billbrod/spatial-frequency-preferences), see the README
there for more details.

## Overview

- Spatial frequency preferences

- Year(s) that the project ran: started gathering pilot data in 2017, this
dataset was gathered in the springs of 2019 and 2020. Paper written in 2020
and 2021, submitted fall 2021.

- Brief overview of the tasks in the experiment: subjects viewed the stimuli,
fixating on the center of the images. A sequence of digits, alternating black
and white, was presented at fixation; subjects pressed a button whenever a
digit repeated. See paper for more details.

- Description of the contents of the dataset:
- Summary:
- 768 Files
- 12 subjects
- 1 session each
- Available tasks:
- sfprescaled
- Available modalities:
- MRI

- Quality assessment of the data: the MRIQC reports for each included scan can
be found [on this project's OSF page](https://osf.io/zrq6b/)

## Methods

### Subjects

Subjects were recruited from graduate students and postdocs at NYU, all
experienced MRI participants.

### Apparatus

Data was gathered on NYU's Center for Brain Imaging's Siemens Prisma 3T MRI
scanner in a shielded room. Data was gathered with subjects lying down, with the
stimuli projected onto a screen above their head.

### Initial setup

When subjects arrived, subjects were briefed on the task, given the experimental
consent form to read and sign, and talked through the screener form.

### Task organization

This experiment has only a single task.

### Task details

Subjects passively viewed the stimuli while performing the distractor task
described above: viewing a stream of alternating black and white digits and
pressing a button whenever a digit repeated. Their button presses were recorded.
Each subject's `events.tsv` files gives the behavioral results ("hit", "miss",
"correct_rejection", or "false_alarm").

### Additional data acquired

No additional data gathered.

### Experimental location

All data gathered at NYU's Center for Brain Imaging in New York, NY.

### Missing data

One subject (sub-wlsubj045) only has 7 of the 12 runs, due to technical issues
that came up during the run. The quality of their GLMdenoise fits and their
final model fits do not appear to vary much from that of the other subjects.