Gagnon_CerebralCortex_2018

Analysis repository for Gagnon et al. (2018) Cerebral Cortex

Dependencies (incomplete list):

• Python 2.7 (Anaconda distribution ~2.3 / 2.4)
• https://github.com/sgagnon/lyman (adapted from https://github.com/mwaskom/lyman)
• https://github.com/sgagnon/lyman-tools
• https://github.com/sgagnon/felix
• https://github.com/sgagnon/fmri_classification
• https://github.com/mwaskom/seaborn
• https://github.com/mwaskom/moss
• FSL
• Freesurfer
• ANTS
• scikit-learn
• nibabel
• nitime
• nipype
• numpy, scipy, matplotlib
• Please contact us for the full list of dependencies (some packages have potential security vulnerabilities)

Directory overview

• Main code to run behavioral task: AP/ap.m and assorted files in scripts
• Behavioral data: AP/data
• Behavioral preprocessing: AP/analysis
• Localizer task/data: localizer
• MRI data processing: SNI (corresponds to /Volumes/group/awagner/sgagnon/AP)
• Statistics: stats (All statistics: AP_results.Rmd)

MRI data/results

• ROI parameter estimates: SNI/analysis/ap_memory_raw/group/roi
  • note: see Archive for trial-wise ROI data
• Links
  • Statistical maps (Neurovault): https://neurovault.org/collections/3173/
  • Raw data: [*TBD: ARCHIVE LINK]

Code references

This repository contains code taken/adapted from the following sources:

https://github.com/amgordon/Gordon_CerCor_2014

License:

Copyright (c) 2013 Alan Gordon, J. Benjamin Hutchinson, Jesse Rissman.

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Also, we'd like to thank Alan Gordon for experimentation code snippets.

https://github.com/garikoitz/hippovol

The MIT License (MIT)

Copyright (c) 2016 garikoitz. Garikoitz Lerma-Usabiaga ([email protected])

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

https://www.mathworks.com/matlabcentral/fileexchange/24484-geom3d

Copyright (c) 2018, INRA All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

• Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
• Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Error bar code

http://www.cookbook-r.com/Graphs/Plotting_means_and_error_bars_(ggplot2)/#Helper%20functions

Experiment code from Brice Kuhl's RIFS Task / Wagner Lab / AM task (in collaboration with Valerie Carr)

This included lists of words (nouns) used as stimuli

Questionnaire code from Amitai Shenhav

Trigger code from the CNI and Kelly Hennigan

labels_intersect_jim.sh

Code from Jim Porter (University of Minnesota) from the Freesurfer message board https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2009-September/011846.html

Inspiration from https://github.com/mwaskom/Waskom_CerebCortex_2017

License

This code is being released with a permissive open-source license. You should feel free to use or adapt the utility code as long as you follow the terms of the license, which are enumerated below.

Copyright (c) 2018

All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.