Difference between revisions of "Modules:ROISeeding-Documentation-3.6"
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* Author1: Raúl San José Estépar, BWH | * Author1: Raúl San José Estépar, BWH | ||
* Contributor1: Alex Yarmakovich, Isomics | * Contributor1: Alex Yarmakovich, Isomics | ||
| − | * Contact: http://lmi.bwh.harvard.edu/~rjosest/address.html] | + | * Contact: [http://lmi.bwh.harvard.edu/~rjosest/address.html] |
===Module Description=== | ===Module Description=== | ||
| − | Labelmap Seeding is a tractography implementation that allows a user to seed tracts from a region of interest (ROI). The ROI is defined as a labelmap and has to be provided by the user. One approach to generate the ROI is by means of the Editor module [ | + | Labelmap Seeding is a tractography implementation that allows a user to seed tracts from a region of interest (ROI). The ROI is defined as a labelmap and has to be provided by the user. One approach to generate the ROI is by means of the Editor module [[Modules:Editor-Documentation-3.6] |
| − | == Usage == | + | ==|Usage == |
===Examples, Use Cases & Tutorials=== | ===Examples, Use Cases & Tutorials=== | ||
* We want to study the white matter integrate across a population for a given tract. ROISeeding can be used to carry this study. | * We want to study the white matter integrate across a population for a given tract. ROISeeding can be used to carry this study. | ||
| − | **First, a region of interest in the tract that is under study has to be defined for each subject, for example by manually delineating the ROI using the Editor module. The Fractional Anisotropy (FA) Volume can be used as reference volume to trace the ROI. The FA volume can be computed using [ | + | **First, a region of interest in the tract that is under study has to be defined for each subject, for example by manually delineating the ROI using the Editor module. The Fractional Anisotropy (FA) Volume can be used as reference volume to trace the ROI. The FA volume can be computed using [[Modules:DiffusionTensorScalarMeasurements-Documentation-3.4|Diffusion Tensor Scalar Measurements]]]. |
| − | **Second, if the DTI volume is not direcly available, the DWI has to be loaded and the tensor has to be created using the [ | + | **Second, if the DTI volume is not direcly available, the DWI has to be loaded and the tensor has to be created using the [[Modules:DiffusionTensorEstimation-Documentation-3.4|| Diffusion Tensor Estimation]]. |
**Third, set up the ROI Seeding using the DTI volume and the ROI labelmap as main volume inputs. | **Third, set up the ROI Seeding using the DTI volume and the ROI labelmap as main volume inputs. | ||
**Fourth, choose the tractography parameters. The stopping criteria are the more important parameters. Depending on the setting different results can be obtained, for example, fiber can be longer or shorter. | **Fourth, choose the tractography parameters. The stopping criteria are the more important parameters. Depending on the setting different results can be obtained, for example, fiber can be longer or shorter. | ||
| Line 38: | Line 38: | ||
The module is very straighforward to use: | The module is very straighforward to use: | ||
| − | * '''Input | + | * '''Input / Output:''' |
| − | * ''' | + | ** Input DTI Volume: set the input DTI volume that is going to be used for tractography. |
| − | * ''' | + | ** Input Label Map: set the labelmap volume that is going to be used for seeding. |
| − | * ''' | + | ** Output Fiber bundle: set the resulting fiber bundle that is going to store the result. |
| + | ** Write Fibers to Disk: option to save the results to disk for further analysis. | ||
| + | ** Output directory: path where the results are saved. | ||
| + | ** File Prefix Name: name that would be used for each output bundle. | ||
| + | * '''Seed Placement Options''' | ||
| + | ** Use Index Space: if selected seed at IJK voxel grid | ||
| + | ** Seed Spacing: spacing in between seed points within in the labelmap (in mm), only matters if use Use Index Space is off. | ||
| + | ** Random grid: use random placement. | ||
| + | ** Linear Measure Start Threshold: place seeds only if linear measure (cl) is above this threshold. | ||
| + | * '''Tractography Seeding Parameters:''' | ||
| + | ** Minimum Length: | ||
| + | ** Maximum Length: | ||
| + | * '''Label Definition:''' | ||
=== Caveats and other limitations === | === Caveats and other limitations === | ||
| − | ROISeeding module does not work when the labelmap dimensions do not match the DTI volume dimensions. The work-around is to resample labelmap using [ | + | *ROISeeding module does not work when the labelmap dimensions do not match the DTI volume dimensions. The work-around is to resample labelmap using [[Modules:ResampleVolume2-Documentation-3.4|| Filtering -> Resample Volume 2]]. |
| + | |||
| + | *ROISeeding module scans the label volume using the "seeding spacing" parameter (mm) as a step. If the label volume has a single slice with labels or separated slices there is a chance that the module can miss labels entirely. To avoid this situation a new parameter UseIndexSpace was added that will force the seeding at the label volume grid. Making "seeding spacing" less than the smallest volume spacing makes the same effect. | ||
== Development == | == Development == | ||
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===Source code & documentation=== | ===Source code & documentation=== | ||
| − | Information about the DTMRI infrastructure in Slicer 3 and related classess can be found [ | + | Information about the DTMRI infrastructure in Slicer 3 and related classess can be found [[Slicer3:DTMRI|here]] |
[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/ Links] to documentation generated by doxygen. | [http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/ Links] to documentation generated by doxygen. | ||
Latest revision as of 02:23, 27 November 2019
Home < Modules:ROISeeding-Documentation-3.6Return to Slicer 3.6 Documentation
Module Name
Labelmap Seeding
General Information
Module Type & Category
Type: CLI
Category: Diffusion MRI Applications
Authors, Collaborators & Contact
- Author1: Raúl San José Estépar, BWH
- Contributor1: Alex Yarmakovich, Isomics
- Contact: [1]
Module Description
Labelmap Seeding is a tractography implementation that allows a user to seed tracts from a region of interest (ROI). The ROI is defined as a labelmap and has to be provided by the user. One approach to generate the ROI is by means of the Editor module [[Modules:Editor-Documentation-3.6]
|Usage
Examples, Use Cases & Tutorials
- We want to study the white matter integrate across a population for a given tract. ROISeeding can be used to carry this study.
- First, a region of interest in the tract that is under study has to be defined for each subject, for example by manually delineating the ROI using the Editor module. The Fractional Anisotropy (FA) Volume can be used as reference volume to trace the ROI. The FA volume can be computed using Diffusion Tensor Scalar Measurements].
- Second, if the DTI volume is not direcly available, the DWI has to be loaded and the tensor has to be created using the | Diffusion Tensor Estimation.
- Third, set up the ROI Seeding using the DTI volume and the ROI labelmap as main volume inputs.
- Fourth, choose the tractography parameters. The stopping criteria are the more important parameters. Depending on the setting different results can be obtained, for example, fiber can be longer or shorter.
Quick Tour of Features and Use
The module is very straighforward to use:
- Input / Output:
- Input DTI Volume: set the input DTI volume that is going to be used for tractography.
- Input Label Map: set the labelmap volume that is going to be used for seeding.
- Output Fiber bundle: set the resulting fiber bundle that is going to store the result.
- Write Fibers to Disk: option to save the results to disk for further analysis.
- Output directory: path where the results are saved.
- File Prefix Name: name that would be used for each output bundle.
- Seed Placement Options
- Use Index Space: if selected seed at IJK voxel grid
- Seed Spacing: spacing in between seed points within in the labelmap (in mm), only matters if use Use Index Space is off.
- Random grid: use random placement.
- Linear Measure Start Threshold: place seeds only if linear measure (cl) is above this threshold.
- Tractography Seeding Parameters:
- Minimum Length:
- Maximum Length:
- Label Definition:
Caveats and other limitations
- ROISeeding module does not work when the labelmap dimensions do not match the DTI volume dimensions. The work-around is to resample labelmap using | Filtering -> Resample Volume 2.
- ROISeeding module scans the label volume using the "seeding spacing" parameter (mm) as a step. If the label volume has a single slice with labels or separated slices there is a chance that the module can miss labels entirely. To avoid this situation a new parameter UseIndexSpace was added that will force the seeding at the label volume grid. Making "seeding spacing" less than the smallest volume spacing makes the same effect.
Development
Dependencies
None
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
Information about the DTMRI infrastructure in Slicer 3 and related classess can be found here
Links to documentation generated by doxygen.
More Information
Acknowledgment
Include funding and other support here.
References
Publications related to this module go here. Links to pdfs would be useful.
