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gradient-decoding

Methods for decoding cortical gradients of functional connectivity

https://github.com/nbclab/gradient-decoding

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Keywords

meta-analysis neuroimaging python
Last synced: 6 months ago · JSON representation ·

Repository

Methods for decoding cortical gradients of functional connectivity

Basic Info
  • Host: GitHub
  • Owner: NBCLab
  • License: apache-2.0
  • Language: Jupyter Notebook
  • Default Branch: main
  • Homepage: https://osf.io/xzfrt/
  • Size: 96.3 MB
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  • Stars: 6
  • Watchers: 4
  • Forks: 0
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Topics
meta-analysis neuroimaging python
Created over 3 years ago · Last pushed about 2 years ago
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Readme License Citation

README.md

gradient-decoding

Methods for decoding cortical gradients of functional connectivity

Summary

This repository contains all code required to reproduce the analyses and figures of the "Methods for decoding cortical gradients of functional connectivity" paper. Please refer to the paper for further details: https://doi.org/10.1162/imaga00081

Workflow

The workflow consists of the following steps:

  1. Functional Connectivity Gradients:
    • HCP S1200 resting-state fMRI data were used to generate functional connectivity and compute the affinity matrix.
    • Diffusion map embedding was applied to identify the principal gradient of functional connectivity.
  2. Segmentation and Gradient Maps:
    • Whole-brain gradient maps were segmented to divide the gradient spectrum into a finite number of brain maps.
    • Three different segmentation approaches were evaluated: percentile-based (PCT), k-means (KMeans), and KDE.
    • Individual segments were transformed into pseudo-activation brain maps for decoding.
    • The three segmentation approaches were evaluated using the silhouette, variance ratio, and cluster separation scores.
  3. Meta-analytic Functional Decoding:
    • Six different meta-analytic decoding strategies were implemented on surface space, derived from three sets of meta-analytic maps (i.e., term-based (Term), LDA, and GCLDA) and two databases (i.e., NS: Neurosynth and NQ: NeuroQuery).
  4. Performance of Decoding Strategies:
    • The resultant 18 different decoding strategies were evaluated using four performance metrics, assessed by comparing correlation profiles, semantic similarity metrics (i.e., information content (IC) and TFIDF), and signal-to-noise ratio (SNR).
  5. Multidimensional Decoding:
    • Finally, we performed a multidimensional decoding using the first four components together.

Fig-01

How to use

1. Install dependencies

In order to execute the workflow (workflow.py), you will need to install all of the Python libraries that are required. The required library and associated versions are available in requirements.txt.

The easiest way to install the requirements is with Conda.

python conda create -p /path/to/gradientdec_env pip python=3.9 conda activate /path/to/gradientdec_env pip install -r requirements.txt

2. Download data files

The analysis workflow is computationally intensive. If a user would like to skip any step, they will need to download the necessary files in data and results from our OSF page: https://osf.io/xzfrt/.

3. Run the workflow

To run the workflow, create a project directory PROJECT_DIR, and execute the command:

python workflow.py --project_dir ${PROJECT_DIR} --n_cores 1

Alternatively, users can adapt and use our SLURM submission script: ./jobs/run_workflow.sh.

sbatch ./jobs/run_workflow.sh

Citation

If you use this code in your research, please acknowledge this work by citing the paper: https://doi.org/10.1162/imaga00081.

Note

The script workflow.py should be used only for reproducibility purposes of the linked paper. In order to perform the proposed analysis in your data, please refer to the Python package Gradec.

Owner

  • Name: Neuroinformatics and Brain Connectivity Lab
  • Login: NBCLab
  • Kind: organization
  • Email: neurolab@fiu.edu
  • Location: Florida International University

A cognitive neuroscience lab led by Drs. Angela Laird and Matthew Sutherland.

Citation (CITATION.cff) 

cff-version: 1.2.0
message: If you use this code, please cite it as below.

title: Methods for decoding cortical gradients of functional connectivity

abstract: |
  Macroscale gradients have emerged as a central principle for understanding functional brain 
  organization. Previous studies have demonstrated that a principal gradient of connectivity in 
  the human brain exists, with unimodal primary sensorimotor regions situated at one end and 
  transmodal regions associated with the default mode network and representative of abstract 
  functioning at the other. The functional significance and interpretation of macroscale gradients 
  remains a central topic of discussion in the neuroimaging community, with some studies 
  demonstrating that gradients may be described using meta-analytic functional decoding techniques. 
  However, additional methodological development is necessary to fully leverage available 
  meta-analytic methods and resources and quantitatively evaluate their relative performance. 
  Here, we conducted a comprehensive series of analyses to investigate and improve the framework 
  of data-driven, meta-analytic methods, thereby establishing a principled approach for gradient 
  segmentation and functional decoding. We found that a two-segment solution determined by a 
  k-means segmentation approach and an LDA-based meta-analysis combined with the NeuroQuery 
  database was the optimal combination of methods for decoding functional connectivity gradients. 
  Finally, we proposed a method for decoding additional components of the gradient decomposition. 
  The current work aims to provide recommendations on best practices and flexible methods for 
  gradient-based functional decoding of fMRI data.

repository-code: https://github.com/NBCLab/gradient-decoding

identifiers:
  - type: doi
    value: https://doi.org/10.1162/imag_a_00081
    description: Methods for decoding cortical gradients of functional connectivity

contact:
  - given-names: Julio A
    family-names: Peraza
    email: jperaza@fiu.edu
    affiliation: Department of Physics, Florida International University, Miami, FL, USA

license: Apache License 2.0

authors:
  - given-names: Julio A
    family-names: Peraza
    orcid: 0000-0003-3816-5903
    affiliation: Department of Physics, Florida International University, Miami, FL, USA
  - given-names: Taylor
    family-names: Salo
    orcid: 0000-0001-9813-3167
    affiliation: Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
  - given-names: Michael C
    family-names: Michael
    orcid: 0000-0002-1860-4449
    affiliation: LTI Engineering and Software, Quebec City, QC, Canada
  - given-names: Katherine L
    family-names: Bottenhorn
    orcid: 0000-0002-7796-8795
    affiliation: Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA
  - given-names: Jean-Baptiste
    family-names: Poline
    orcid: 0000-0002-9794-749X
    affiliation: Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
  - given-names: Jérôme
    family-names: Dockès
    orcid: 0000-0002-5304-2496
    affiliation: Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
  - given-names: James D
    family-names: Kent
    orcid: 0000-0002-4892-2659
    affiliation: Department of Psychology, University of Texas at Austin, Austin, TX, USA
  - given-names: Jessica E
    family-names: Bartley
    orcid: 0000-0001-7269-9701
    affiliation: Department of Physics, Florida International University, Miami, FL, USA
  - given-names: Jessica S
    family-names: Flannery
    orcid: 0000-0003-3274-1578
    affiliation: Department of Psychology and Neuroscience, University of North Carolina, Chapel Hill, NC, USA
  - given-names: Lauren D
    family-names: Hill-Bowen
    orcid: 0000-0002-9817-7757
    affiliation: Department of Psychology, Florida International University, Miami, FL, USA
  - given-names: Rosario
    family-names: Pintos Lobo
    orcid: 0000-0002-7679-1385
    affiliation: Department of Psychology, Florida International University, Miami, FL, USA
  - given-names: Ranjita
    family-names: Poudel
    orcid: 0000-0003-4343-1153
    affiliation: Department of Health Outcomes and Behavior, Moffitt Cancer Center, Tampa, FL, USA
  - given-names: Kimberly L
    family-names: Ray
    orcid: 0000-0003-1302-2834
    affiliation: Department of Psychology, University of Texas at Austin, Austin, TX, USA
  - given-names: Jennifer L
    family-names: Robinson
    orcid: 0000-0001-7389-3047
    affiliation: Department of Psychology, Auburn University, Auburn, AL, USA
  - given-names: Robert W
    family-names: Laird
    affiliation: Department of Physics, Florida International University, Miami, FL, USA
  - given-names: Matthew T
    family-names: Sutherland
    orcid: 0000-0002-6091-4037
    affiliation: Department of Psychology, Florida International University, Miami, FL, USA
  - given-names: Alejandro
    family-names: de la Vega
    orcid: 0000-0001-9062-3778
    affiliation: Department of Psychology, University of Texas at Austin, Austin, TX, USA
  - given-names: Angela R
    family-names: Laird
    orcid: 0000-0003-3379-8744
    affiliation: Department of Physics, Florida International University, Miami, FL, USA

preferred-citation:
  authors:
    - given-names: Julio A
      family-names: Peraza
      orcid: 0000-0003-3816-5903
      affiliation: Department of Physics, Florida International University, Miami, FL, USA
    - given-names: Taylor
      family-names: Salo
      orcid: 0000-0001-9813-3167
      affiliation: Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
    - given-names: Michael C
      family-names: Michael
      orcid: 0000-0002-1860-4449
      affiliation: LTI Engineering and Software, Quebec City, QC, Canada
    - given-names: Katherine L
      family-names: Bottenhorn
      orcid: 0000-0002-7796-8795
      affiliation: Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA
    - given-names: Jean-Baptiste
      family-names: Poline
      orcid: 0000-0002-9794-749X
      affiliation: Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
    - given-names: Jérôme
      family-names: Dockès
      orcid: 0000-0002-5304-2496
      affiliation: Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
    - given-names: James D
      family-names: Kent
      orcid: 0000-0002-4892-2659
      affiliation: Department of Psychology, University of Texas at Austin, Austin, TX, USA
    - given-names: Jessica E
      family-names: Bartley
      orcid: 0000-0001-7269-9701
      affiliation: Department of Physics, Florida International University, Miami, FL, USA
    - given-names: Jessica S
      family-names: Flannery
      orcid: 0000-0003-3274-1578
      affiliation: Department of Psychology and Neuroscience, University of North Carolina, Chapel Hill, NC, USA
    - given-names: Lauren D
      family-names: Hill-Bowen
      orcid: 0000-0002-9817-7757
      affiliation: Department of Psychology, Florida International University, Miami, FL, USA
    - given-names: Rosario
      family-names: Pintos Lobo
      orcid: 0000-0002-7679-1385
      affiliation: Department of Psychology, Florida International University, Miami, FL, USA
    - given-names: Ranjita
      family-names: Poudel
      orcid: 0000-0003-4343-1153
      affiliation: Department of Health Outcomes and Behavior, Moffitt Cancer Center, Tampa, FL, USA
    - given-names: Kimberly L
      family-names: Ray
      orcid: 0000-0003-1302-2834
      affiliation: Department of Psychology, University of Texas at Austin, Austin, TX, USA
    - given-names: Jennifer L
      family-names: Robinson
      orcid: 0000-0001-7389-3047
      affiliation: Department of Psychology, Auburn University, Auburn, AL, USA
    - given-names: Robert W
      family-names: Laird
      affiliation: Department of Physics, Florida International University, Miami, FL, USA
    - given-names: Matthew T
      family-names: Sutherland
      orcid: 0000-0002-6091-4037
      affiliation: Department of Psychology, Florida International University, Miami, FL, USA
    - given-names: Alejandro
      family-names: de la Vega
      orcid: 0000-0001-9062-3778
      affiliation: Department of Psychology, University of Texas at Austin, Austin, TX, USA
    - given-names: Angela R
      family-names: Laird
      orcid: 0000-0003-3379-8744
      affiliation: Department of Physics, Florida International University, Miami, FL, USA

  title: "Methods for decoding cortical gradients of functional connectivity"
  doi: 10.1162/imag_a_00081
  date-released: 2024-02-02
  url: "https://doi.org/10.1162/imag_a_00081"
  journal: Imaging Neuroscience
  type: article

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Dependencies

requirements.txt pypi
  • brainspace ==0.1.10
  • gradec ==0.0.1rc3
  • ipykernel ==6.23.1
  • mapalign ==0.3.0
  • netneurotools ==0.2.3
  • neuromaps ==0.0.4
  • nimare ==0.1.0
  • scikit-learn ==1.2.2
  • scipy ==1.7.3
  • seaborn ==0.11.0
  • surfplot ==0.2.0
  • wordcloud ==1.9.2