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The Paper

This repository includes scripts and data for the following paper:

Cooper, R. & Ritchey, M. (2019). Cortico-hippocampal network connections support the multidimensional quality of episodic memory. eLife, 8, e45591, doi:10.7554/eLife.45591

Abstract

Episodic memories reflect a bound representation of multimodal features that can be reinstated with varying levels of precision. Yet little is known about how brain networks involved in memory, including the hippocampus and posterior-medial (PM) and anterior-temporal (AT) cortical systems, functionally interact to support the quality and the content of recollection. Participants learned color, spatial, and emotion associations of objects, later reconstructing the visual features using a continuous color spectrum and 360° panorama scenes. Behaviorally, dependencies in memory were observed for the gist but not precision of these event associations. Supporting this integration, hippocampus, AT, and PM regions showed increased inter-network connectivity and reduced modularity during retrieval compared to encoding. These network connections, particularly to hippocampus, tracked a multidimensional, continuous measure of objective memory quality. Moreover, distinct patterns of connectivity tracked item color precision and spatial memory precision. These findings demonstrate not only how hippocampal-cortical connections reconfigure during episodic retrieval, but how such dynamic interactions might flexibly support the multidimensional quality of remembered events.

Resources

Psychtoolbox task scripts are included in the task folder. The stimuli used in the experiment can be obtained from the following links: objects, panorama scenes, and sounds.

I have also shared a few key analysis scripts in the analysis folder along with some corresponding data files and reports.

The general flow of the included analysis scripts is as follows:

  • Analyze behavioral data: Orbit-fMRI-Behavior_Paper.Rmd
    • The formatted report with code can be found here. This contains all analysis output from behavioral data in Behavioral_data.csv.
  • Analyze univariate data: Orbit-fMRI-Univariate_Paper.Rmd. This script analyzes first level betas in Univariate_MemoryQuality_data.csv, reflecting the change in mean ROI activity with increasing memory quality.
    • The analysis output and code can be found here.
  • Analyze background connectivity data:
    • Run the first level analysis using the CONN toobox: conn_batch_firstlevel_background.m. This script requires that all task regressors have already been generated.
    • Analyze the first level connectivity data: Orbit-fMRI-BackgroundConnectivity_Paper.Rmd. This script calls functions in background_functions_paper.R to format, analyze, and visualize the connectivity matrices at the group level.
    • The analysis output and code can be found here.
    • First level ROIxROI connectivity matrices for encoding and retrieval tasks can be found in Background_connectivity_data.RData.
  • Analyze memory-modulated connectivity (gPPI) data:
    • Run the first level analysis using CONN: conn_batch_firstlevel_memorygPPI.m. This script requires that all task regressors have already been generated.
    • Analyze the first level connectivity data: Orbit-fMRI-MemorygPPI_Paper.Rmd. This script calls functions in gPPI_functions_paper.R to format, analyze, and visualize the network and ROI connectivity matrices at the group level.
    • The analysis output and code can be found here, which tests changes in connectivity with i) overall memory quality, ii) color memory precision, and iii) scene memory precision.
    • First level ROIxROI connectivity matrices (beta estimates for the PPI regressor) for each memory modulator can be found in Memory_gPPI_data.RData.
    • The group-level results of the hippocampus seed to voxel analysis (change in whole-brain hippocampal connectivity with increasing memory quality) are also provided as an spmT.nii file: HippSeed_wholebrain_MemoryQuality_spmT.nii.

License

All data included in this project is licensed under the CC BY 4.0 license, and all code is licensed under the MIT license.

Comments?

Please direct any comments to Rose Cooper, rose.cooper at bc.edu. Please feel free to use any of these scripts. Unfortunately I cannot provide support for you to adapt them to your own data. Notice a bug? Please tell me.

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Collection of scripts and data files for an fMRI functional connectivity study of item and spatial context memory precision

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