software.qmd

---
title: "Poldracklab Software and Data"
format:
  html:
    page-layout: full
---


Our lab endeavors to make all of our research code openly available. None of this code is guaranteed to work outside of our local environment, and most of it is not built for portability, but if you use it and find any bugs, please let us know. Unless otherwise noted, all code is released under the unrestrictive [MIT License](http://opensource.org/licenses/MIT)

For additional information on our organized software development projects,
see [Informatics projects](projects.md#informatics-projects).

## Github repositories

The Poldrack lab manages several GitHub organizations:

- [Poldrack Lab at Stanford](https://github.com/poldracklab)
- [OpenNeuro.org](https://github.com/OpenNeuroOrg)
- [The Experiment Factory](https://github.com/expfactory)
- [The Cognitive Atlas](https://github.com/CognitiveAtlas)

We are currently or have been heavily involved in the following organizations:

- [Brain Imaging Data Structure](https://github.com/bids-standard)
- [NeuroVault](https://github.com/neurovault)
- [NiPreps](https://github.com/nipreps)
- [TemplateFlow](https://github.com/templateflow)

We also contribute to greater and lesser extents to many other projects, including:

- [The Nipy community](https://github.com/nipy)
- [Nipype](https://github.com/nipype)
- [Nilearn](https://github.com/nilearn)

For individual members' GitHub profiles, see [Lab members](people.md).

## Software for tasks used in lab publications
- Many of our recent tasks are housed in the [Experiment Factory](https://expfactory.github.io/)
- [mixed gambles task](http://web.stanford.edu/group/poldracklab/software/mixed_gambles_task.zip) (demo and scanning script from task used in Tom et al., 2007)

## Task software used in Consortium for Neuropsychiatric Phenomics (CNP)
  - ​Users of these tasks should include the following acknowledgment in any resulting publications: Development of this software was supported by the Consortium for Neuropsychiatric Phenomics (NIH Roadmap for Medical Research grants UL1-DE019580, RL1MH083269, RL1DA024853, PL1MH083271.
  - [Balloon Analog Risk task](http://web.stanford.edu/group/poldracklab/software/BART.zip) (demo and scanning script)
  - [Breath holding task](http://web.stanford.edu/group/poldracklab/software/BHT.zip)
  - Paired Associate Memory
  - [Spatial working memory capacity](http://web.stanford.edu/group/poldracklab/software/SCAP.zip)
  - [Stop Signal task](http://web.stanford.edu/group/poldracklab/software/STOPSIG.zip)
  - [Task switching](http://web.stanford.edu/group/poldracklab/software/TASKSWITCH.zip)


## Data/code/OSF pages for published papers

```{python}
#| echo: false
#| output: asis
#| warning: false
#| message: false

# this code uses academicdb to put together a list of publications
# with data/code/osf pages
import os
try:
    from datetime import date
    from contextlib import suppress
    from academicdb.dbbuilder import setup_db
    from academicdb.utils import escape_characters_for_latex
    from academicdb.render_pubs import get_publications
    import logging
    import argparse

    configfile = 'config.toml'
    if not os.path.exists(configfile):
        raise FileNotFoundError(
            f'You must first set up the config.toml file'
        )

    db = setup_db(configfile)

    pubs = [i for i in db.get_collection('publications') if 'links' in i]

    print(get_publications(pubs))
except Exception:
    if not os.getenv("POLDRACKLAB_IGNORE_FAILURE"):
        raise

```