run_bidsify

Internal function to run bidsify on a single eye

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

run_bidsify function

<dl><dt>eyeris</dt>
<dd>An eyeris object</dd>
<dt>save_all</dt>
<dd>Whether to save all data</dd>
<dt>epochs_list</dt>
<dd>A list of epochs to include</dd>
<dt>merge_epochs</dt>
<dd>Whether to merge epochs</dd>
<dt>bids_dir</dt>
<dd>The directory to save the bids data</dd>
<dt>participant_id</dt>
<dd>The participant id</dd>
<dt>session_num</dt>
<dd>The session number</dd>
<dt>task_name</dt>
<dd>The task name</dd>
<dt>run_num</dt>
<dd>The run number</dd>
<dt>merge_runs</dt>
<dd>Whether to merge runs</dd>
<dt>save_raw</dt>
<dd>Whether to save raw data</dd>
<dt>html_report</dt>
<dd>Whether to generate an html report</dd>
<dt>report_seed</dt>
<dd>The seed for the report</dd>
<dt>report_epoch_grouping_var_col</dt>
<dd>The column to use for grouping epochs in the report</dd>
<dt>eye_suffix</dt>
<dd>The suffix to add to the eye data</dd>
<dt>verbose</dt>
<dd>Whether to print verbose output</dd>
<dt>raw_binocular_object</dt>
<dd>The raw binocular object</dd></dl>

Arguments

Internal function to run bidsify on a single eye — run_bidsify

<dl>

<dt>eyeris</dt>
<dd>An eyeris object</dd>


<dt>save_all</dt>
<dd>Whether to save all data</dd>


<dt>epochs_list</dt>
<dd>A list of epochs to include</dd>


<dt>merge_epochs</dt>
<dd>Whether to merge epochs</dd>


<dt>bids_dir</dt>
<dd>The directory to save the bids data</dd>


<dt>participant_id</dt>
<dd>The participant id</dd>


<dt>session_num</dt>
<dd>The session number</dd>


<dt>task_name</dt>
<dd>The task name</dd>


<dt>run_num</dt>
<dd>The run number</dd>


<dt>merge_runs</dt>
<dd>Whether to merge runs</dd>


<dt>save_raw</dt>
<dd>Whether to save raw data</dd>


<dt>html_report</dt>
<dd>Whether to generate an html report</dd>


<dt>report_seed</dt>
<dd>The seed for the report</dd>


<dt>report_epoch_grouping_var_col</dt>
<dd>The column to use for grouping epochs in the report</dd>


<dt>eye_suffix</dt>
<dd>The suffix to add to the eye data</dd>


<dt>verbose</dt>
<dd>Whether to print verbose output</dd>


<dt>raw_binocular_object</dt>
<dd>The raw binocular object</dd>

</dl>

run_bidsify: Internal function to run bidsify on a single eye

Description

Usage

Value

Arguments