visualqc 0.6.3 documentation

Gallery - Freesurfer (labels filled)

Gallery - Freesurfer (labels filled)
Gallery - Freesurfer Parcellation
Gallery - Functional MRI scan - artefact detection and rating 

Table Of Contents

  • VisualQC
    • Use-cases supported
    • Features
    • Manual
    • Galleries
    • Contributions
    • Citations
  • Installation
    • Stable release
    • Requirements
    • From sources
  • Use-cases supported
    • Structural MRI use-cases
    • Functional MRI use-cases
    • Diffusion MRI use-cases
    • Registration/Alignment use-cases
  • Recommended Usage
    • General suggestions:
    • For Freesurfer outputs:
    • Alignment checks (Registration quality)
  • Command line usage
  • Data formats and requirements
  • Review interface
    • Common elements
    • Review interface - Freesurfer
    • Review interface - Anatomical / T1w MRI
    • Review interface - Registration
    • Review interface - Functional MRI
    • Review interface - Diffusion MRI
    • Review interface - Defacing
  • Gallery - Freesurfer Parcellation
  • Gallery - Freesurfer (labels filled)
  • Gallery - Functional MRI scan - artefact detection and rating
  • Gallery - Diffusion MRI artefact detection and rating
  • Gallery - Registration : comparison of spatial alignment
  • Gallery - Defacing algorithm accuracy
  • Gallery - Segmentation/ROI - anatomical accuracy evaluation
  • Gallery - Structural T1w MRI - artefact detection and rating
  • Command line usage - Freesurfer
    • Input and output
    • Overlay options
    • Outlier detection
    • Layout options
    • Workflow
  • Command line usage - Defacing
    • Input and output
  • Command line usage - Functional MRI
    • Input and output
    • Preprocessing
    • Outlier detection
    • Layout options
    • Workflow
  • Command line usage - Diffusion MRI
    • Input and output
    • Preprocessing
    • Visualization
    • Outlier detection
    • Layout options
    • Workflow
  • Command line usage - Alignment
    • Input and output
    • Visualization
    • Outlier detection
    • Layout options
    • Workflow
  • Command line usage - T1w MRI
    • Input and output
    • Visualization
    • Outlier detection
    • Layout options
    • Workflow
  • Generating Screenshots
  • Example usage - Freesurfer
    • Generating and Downloading Required Files from a remote SSH server
  • Example usage - Segmentation
  • Example usage - Defacing
  • Example usage - Functional MRI
  • Example usage - Diffusion MRI
  • Example usage - Alignment
  • Example usage - T1w MRI
  • Contributing
    • Types of Contributions
      • Report Bugs
      • Fix Bugs
      • Implement Features
      • Write Documentation
      • Submit Feedback
    • Get Started!
    • Pull Request Guidelines
    • Tips
  • Citation
  • Credits
    • Development Lead
    • Contributors
  • VisualQC
    • Use-cases supported
    • Features
    • Manual
    • Galleries
    • Contributions
    • Citations
  • Installation
    • Stable release
    • Requirements
    • From sources
  • Use-cases supported
    • Structural MRI use-cases
    • Functional MRI use-cases
    • Diffusion MRI use-cases
    • Registration/Alignment use-cases
  • Recommended Usage
    • General suggestions:
    • For Freesurfer outputs:
    • Alignment checks (Registration quality)
  • Command line usage
  • Data formats and requirements
  • Review interface
    • Common elements
    • Review interface - Freesurfer
    • Review interface - Anatomical / T1w MRI
    • Review interface - Registration
    • Review interface - Functional MRI
    • Review interface - Diffusion MRI
    • Review interface - Defacing
  • Gallery - Freesurfer Parcellation
  • Gallery - Freesurfer (labels filled)
  • Gallery - Functional MRI scan - artefact detection and rating
  • Gallery - Diffusion MRI artefact detection and rating
  • Gallery - Registration : comparison of spatial alignment
  • Gallery - Defacing algorithm accuracy
  • Gallery - Segmentation/ROI - anatomical accuracy evaluation
  • Gallery - Structural T1w MRI - artefact detection and rating
  • Command line usage - Freesurfer
    • Input and output
    • Overlay options
    • Outlier detection
    • Layout options
    • Workflow
  • Command line usage - Defacing
    • Input and output
  • Command line usage - Functional MRI
    • Input and output
    • Preprocessing
    • Outlier detection
    • Layout options
    • Workflow
  • Command line usage - Diffusion MRI
    • Input and output
    • Preprocessing
    • Visualization
    • Outlier detection
    • Layout options
    • Workflow
  • Command line usage - Alignment
    • Input and output
    • Visualization
    • Outlier detection
    • Layout options
    • Workflow
  • Command line usage - T1w MRI
    • Input and output
    • Visualization
    • Outlier detection
    • Layout options
    • Workflow
  • Generating Screenshots
  • Example usage - Freesurfer
    • Generating and Downloading Required Files from a remote SSH server
  • Example usage - Segmentation
  • Example usage - Defacing
  • Example usage - Functional MRI
  • Example usage - Diffusion MRI
  • Example usage - Alignment
  • Example usage - T1w MRI
  • Contributing
    • Types of Contributions
      • Report Bugs
      • Fix Bugs
      • Implement Features
      • Write Documentation
      • Submit Feedback
    • Get Started!
    • Pull Request Guidelines
    • Tips
  • Citation
  • Credits
    • Development Lead
    • Contributors

Gallery - Freesurfer (labels filled)¶

Freesufer’s cortical parcellation against the original MRI (note one axis is zoomed-in):

_images/cortical_zoomed_in.png

In the second screenshot, we show the use case for a single label (subcortical segmentation, tissue class or cortical ROI) - shown here is hippocampus:

_images/hippocampus_not_zoomed_in.png

Focusing on multiple subcortical structures:

_images/subcortical_multiple.png

And you can add as many ROIs as you like:

_images/subcortical_even_more.png

ROIs could be from anywhere in the MRI (including big cortical labels too!). For example, let’s look at posterior cingulate (label 1023 in Freesurfer ColorLUT) in the left hemi-sphere :

_images/lh-posteriorcingulate_1023.png

And, how about insula?

_images/insula_1035.png

You can also combine as many cortical ROIs as you wish and zoom in on them to get every detail you need to judge their accuracy:

_images/single_label_cortical_zoomed_in.png
© Copyright 2017, Pradeep Reddy Raamana. Built with Sphinx 6.1.3 and the Sizzle theme.