Add Pycortex visualization tutorial.md

[AbabababaSmart]

Summary by Sourcery

Add a comprehensive markdown tutorial for visualizing the NSD fMRI dataset using Pycortex

Documentation:

• Introduce a detailed step-by-step guide covering data acquisition, Pycortex installation, surface database generation, and flatmap visualization
• Document ROI annotation using Inkscape and XLaunch workflow
• Provide prebuilt Pycortex surface databases for NSD participants and troubleshooting common issues
• Outline alternative MNI-based workflow for visualizing non-NSD datasets

[sourcery-ai]

Reviewer's Guide

Introduces a comprehensive markdown tutorial that guides users through visualizing the NSD dataset with Pycortex, covering data setup, surface database generation, core visualization code, ROI annotations, and troubleshooting.

Flow diagram for NSD dataset visualization workflow

flowchart TD
    A["Download NSD data from AWS S3"] --> B["Download surface database files (FreeSurfer)"]
    B --> C["Download reference fMRI file (meanbeta.nii.gz)"]
    C --> D["Generate Pycortex database for each participant"]
    D --> E["Align functional data to anatomical surface"]
    E --> F["Prepare data to project (numpy array)"]
    F --> G["Run core visualization code (cortex.Volume, cortex.quickflat.make_figure)"]
    G --> H["Download ROI files"]
    H --> I["Annotate ROIs using Inkscape via XLaunch"]
    I --> J["Save overlays.svg with ROI annotations"]
    J --> K["Re-run visualization code to display ROIs"]
    K --> L["Troubleshooting (rotation, curvature, etc.)"]
    L --> M["(Optional) Download pre-annotated surface databases"]
    M --> N["Visualize with pre-annotated ROIs"]

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File-Level Changes

Change	Details	Files
Add comprehensive Pycortex visualization tutorial for NSD dataset	Preface with overview and motivation NSD dataset introduction and download instructions Pycortex library overview and flatmap workflow Prerequisite files setup for raw data and surface database Core volume-to-flatmap code examples ROI labeling workflow with Inkscape and XLaunch Public release instructions for prebuilt surface databases Common issues troubleshooting and alternative workflows	Pycortex visualization tutorial.md

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[sourcery-ai]

Hey there - I've reviewed your changes and they look great!

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