Difference between revisions of "Modules:StochasticTractography-Documentation-3.4"

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** You are not obliged to set the ROIs or the white matter mask to smooth the DWI, create the brain mask and the tensor. These 3 steps just require a DWI.  
 
** You are not obliged to set the ROIs or the white matter mask to smooth the DWI, create the brain mask and the tensor. These 3 steps just require a DWI.  
 
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** Advice: you can enable solely that functionality and compute several times with different parameters till you're satisfied with the output.   
 
** Advice: you can enable solely that functionality and compute several times with different parameters till you're satisfied with the output.   
 
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This filter allows to remove ventricles from the tractography domain and most of the outside of the brain. This impacts positively the speed without impairing the tractography.  
 
This filter allows to remove ventricles from the tractography domain and most of the outside of the brain. This impacts positively the speed without impairing the tractography.  
 
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** FA, mode and trace are sent as scalar volumes and inserted in the MRML tree.
 
** FA, mode and trace are sent as scalar volumes and inserted in the MRML tree.
 
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** Stopping criteria: FA is used as the stopping criteria. Advice: as ROIs are defined in the grey matter FA are generally very low, therefore do not use generally.
 
** Stopping criteria: FA is used as the stopping criteria. Advice: as ROIs are defined in the grey matter FA are generally very low, therefore do not use generally.
 
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* '''Connectivity Map panel:'''
 
* '''Connectivity Map panel:'''
 
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Revision as of 00:39, 16 April 2009

Home < Modules:StochasticTractography-Documentation-3.4
Return to Slicer 3.4 Documentation

Module Name

Stochastic Tractography

Corpus callosum with stochastic tractography
Corpus callosum lateral projections

General Information

Module Type & Category

Type: Interactive

Category: DTI

Authors, Collaborators & Contact

  • Author: Julien von Siebenthal
  • Contributor: Steve Pieper
  • Contact: jvs@bwh.harvard.edu

Module Description

As a main purpose, the stochastic tractography module helps to evaluate connectivity between two regions of interest (ROIs) of the brain. These ROIs define generally grey matter regions having a specific neurophysiological function. Extensively, study involving more than two regions could still be done by pairing the regions two by two.

Usage

  • You want to study fiber path from a single region of interest (ROI)
  • You want to evaluate connectivity between two ROIs

Description

Stochastic tractography panel

With the stochastic tractography module, you can:

  • Feature 1 : smooth using a Half Width Full Maximum gaussian filter
Smoothing step
  • Feature 2 : generate a brain mask
Brain mask step
  • Feature 3 : create a DTI (Diffusion Tensor Image) tensor
Tensor step
  • Feature 4 : produce different measures based on the tensor like fractional anistropy (FA), mode and trace
Tensor step: FA
Tensor step: mode
Tensor step: trace
  • Feature 5 : produce connection maps in case 2 ROIs are given without ROI filtering
    • showing union and intersection of both maps from region A to region B and B to A
Union of A to B and B to A
Intersection of A to B and B to A
  • Feature 6 : produce connection maps in case 2 ROIs are given with ROI filtering
    • showing only tracts connecting region A to region B and B to A
ROI filtering
ROI filtering from A to B
ROI filtering from B to A

Quick Tour of Features and Use

  • IO panel:
    • Input DWI Volume: the DWI is loaded through the Volume module - it is th only mandatory input.
    • Input ROI Volume (A/B): only 1 ROI is needed to achieve a tractography. If you want to evaluate the connection between two regions, you will give both ROIs.
    • Input WM Volume: a white matter mask can be given as input to use ones provided by other tools or Slicer modules - it will supersede the brain mask even if enabled. Be mindful in setting a WM: tractography results can be impaired by a too restrictive WM.
    • You are not obliged to set the ROIs or the white matter mask to smooth the DWI, create the brain mask and the tensor. These 3 steps just require a DWI.
IO step
  • Smoothing panel:
    • Gaussian FWHM: this filter defines a Full Width Half Maximum. You can define it for each direction in modifying each component of the 3-vector.
    • Advice: you can enable solely that functionality and compute several times with different parameters till you're satisfied with the output.
Smoothing step
  • Brain Mask panel:
    • Lower/Higher Brain Threshold: this filter is based on a simple level set segmentation - intensities of the baseline lying between the two values will be represented, others are set to 0.

This filter allows to remove ventricles from the tractography domain and most of the outside of the brain. This impacts positively the speed without impairing the tractography.

Brain mask step
  • Diffusion Tensor panel:
    • Important: this step is not mandatory. It is here to evaluate the whole tensor and achieve measurements like FA, mode or trace. You did not need it to achieve tractography.
    • FA, mode and trace are sent as scalar volumes and inserted in the MRML tree.
Tensor step
  • Tractography panel:
    • Total tracts: number of generated tracts per voxel.
    • Maximum tract length (mm): set the maximum length tracts could reach.
    • Step size (mm): is the step length for the update vector.
    • Use spacing: must be used with caution - activate spacing to the update vector.
    • Stopping criteria: FA is used as the stopping criteria. Advice: as ROIs are defined in the grey matter FA are generally very low, therefore do not use generally.
Tractography step
  • Connectivity Map panel:
Connectivity step

Development

Dependencies

Volumes

Known bugs

Follow this link to the Slicer3 bug tracker.


Usability issues

Follow this link to the Slicer3 bug tracker. Please select the usability issue category when browsing or contributing.

Source code & documentation

More Information

Acknowledgment

National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149 (to Ron Kikinis, Marek Kubicki).

References

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