export_confounds_to_csv

Exports each block's confounds data to a separate CSV file and/or database table.
Each file will contain all pupil steps (e.g., pupil_raw, pupil_clean)
as rows, with confound metrics as columns.

internal

Pupillometry offers a non-invasive window into the mind and has been used extensively as a psychophysiological readout of arousal signals linked with cognitive processes like attention, stress, and emotional states [Clewett et al. (2020) <doi:10.1038/s41467-020-17851-9>; Kret & Sjak-Shie (2018) <doi:10.3758/s13428-018-1075-y>; Strauch (2024) <doi:10.1016/j.tins.2024.06.002>]. Yet, despite decades of pupillometry research, many established packages and workflows to date lack design patterns based on Findability, Accessibility, Interoperability, and Reusability (FAIR) principles [see Wilkinson et al. (2016) <doi:10.1038/sdata.2016.18>]. 'eyeris' provides a modular, performant, and extensible preprocessing framework for pupillometry data with BIDS-like organization and interactive output reports [Esteban et al. (2019) <doi:10.1038/s41592-018-0235-4>; Gorgolewski et al. (2016) <doi:10.1038/sdata.2016.44>]. Development was supported, in part, by the Stanford Wu Tsai Human Performance Alliance, Stanford Ric Weiland Graduate Fellowship, Stanford Center for Mind, Brain, Computation and Technology, NIH National Institute on Aging Grants (R01-AG065255, R01-AG079345), NSF GRFP (DGE-2146755), McKnight Brain Research Foundation Clinical Translational Research Scholarship in Cognitive Aging and Age-Related Memory Loss, American Brain Foundation, and the American Academy of Neurology.

Shawn Schwartz

eyeris

Flexible, Extensible, & Reproducible Pupillometry Preprocessing

export_confounds_to_csv function

<dl><dt>confounds_list</dt>
<dd>A nested list structure containing confounds data</dd>
<dt>output_dir</dt>
<dd>The directory where CSV files will be saved</dd>
<dt>filename_prefix</dt>
<dd>Either a string prefix for filenames or a function
that takes a block name and returns a prefix</dd>
<dt>verbose</dt>
<dd>A flag to indicate whether to print progress messages</dd>
<dt>run_num</dt>
<dd>The run number (if NULL, will be extracted from block names)</dd>
<dt>csv_enabled</dt>
<dd>Whether to write CSV files (default TRUE)</dd>
<dt>db_con</dt>
<dd>Database connection object (NULL if database disabled)</dd>
<dt>sub</dt>
<dd>Subject ID for database metadata</dd>
<dt>ses</dt>
<dd>Session ID for database metadata</dd>
<dt>task</dt>
<dd>Task name for database metadata</dd>
<dt>eye_suffix</dt>
<dd>Eye suffix for binocular data (e.g., "eye-L", "eye-R")</dd>
<dt>epoch_label</dt>
<dd>Epoch label for epoched data (added as column)</dd></dl>

Arguments

Export confounds data to CSV files and/or database — export_confounds_to_csv

<dl>

<dt>confounds_list</dt>
<dd>A nested list structure containing confounds data</dd>


<dt>output_dir</dt>
<dd>The directory where CSV files will be saved</dd>


<dt>filename_prefix</dt>
<dd>Either a string prefix for filenames or a function
that takes a block name and returns a prefix</dd>


<dt>verbose</dt>
<dd>A flag to indicate whether to print progress messages</dd>


<dt>run_num</dt>
<dd>The run number (if NULL, will be extracted from block names)</dd>


<dt>csv_enabled</dt>
<dd>Whether to write CSV files (default TRUE)</dd>


<dt>db_con</dt>
<dd>Database connection object (NULL if database disabled)</dd>


<dt>sub</dt>
<dd>Subject ID for database metadata</dd>


<dt>ses</dt>
<dd>Session ID for database metadata</dd>


<dt>task</dt>
<dd>Task name for database metadata</dd>


<dt>eye_suffix</dt>
<dd>Eye suffix for binocular data (e.g., "eye-L", "eye-R")</dd>


<dt>epoch_label</dt>
<dd>Epoch label for epoched data (added as column)</dd>

</dl>

export_confounds_to_csv: Export confounds data to CSV files and/or database

Description

Usage

Value

Arguments