Modules:ROISeeding-Documentation-3.4 - Revision history

Grundlett: Text replacement - "\[http:\/\/www\.slicer\.org\/slicerWiki\/index\.php\/([^ ]+) ([^]]+)]" to "$2"

2019-11-27T02:26:27Z

Text replacement - "\[http:\/\/www\.slicer\.org\/slicerWiki\/index\.php\/([^ ]+) ([^]]+)]" to "$2"

Nicole: /* Source code & documentation */

2010-01-15T22:14:24Z

Source code & documentation

Marianna at 19:29, 26 May 2009

2009-05-26T19:29:04Z

Alexy: /* Module Name */

2009-04-05T17:45:45Z

Module Name

Raul at 19:22, 17 March 2009

2009-03-17T19:22:15Z

Raul at 19:20, 17 March 2009

2009-03-17T19:20:46Z

Raul at 19:19, 17 March 2009

2009-03-17T19:19:04Z

Raul: /* Examples, Use Cases & Tutorials */

2009-03-17T14:03:44Z

Examples, Use Cases & Tutorials

Raul at 13:52, 17 March 2009

2009-03-17T13:52:16Z

Raul at 13:50, 17 March 2009

2009-03-17T13:50:07Z

@@ Line 30: / Line 30: @@
 * 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 [http://www.slicer.org/slicerWiki/index.php/Modules:DiffusionTensorScalarMeasurements-Documentation-3.4 Diffusion Tensor Scalar Measurements].
+**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 [http://www.slicer.org/slicerWiki/index.php/Modules:DiffusionTensorEstimation-Documentation-3.4 | Diffusion Tensor Estimation].
+**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.
 **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 44: / Line 44: @@
 === 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 [http://www.slicer.org/slicerWiki/index.php/Modules:ResampleVolume2-Documentation-3.4 | Filtering -> Resample Volume 2].
+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]].
 == Development ==
@@ Line 63: / Line 63: @@
 ===Source code & documentation===
-Information about the DTMRI infrastructure in Slicer 3 and related classess can be found [http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI here]
+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.

@@ Line 65: / Line 65: @@
 Information about the DTMRI infrastructure in Slicer 3 and related classess can be found [http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI here]
-[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.
+[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/ Links] to documentation generated by doxygen.
 == More Information ==

@@ Line 1: / Line 1: @@
 [[Documentation-3.4|Return to Slicer 3.4 Documentation]]
 __NOTOC__
 ===Module Name===

@@ Line 2: / Line 2: @@
 __NOTOC__
 ===Module Name===
-MyModule
+Labelmap Seeding
 {|

@@ Line 61: / Line 61: @@
 ===Source code & documentation===
-Customize following [http://www.na-mic.org/ViewVC/index.cgi/ links] for your module.
+Information about the DTMRI infrastructure in Slicer 3 and related classess can be found [http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI here]
 [http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.

@@ Line 5: / Line 5: @@
 {|
-|[[Image:screenshotBlank.png|thumb|280px|Caption 1]]
+|[[Image:roi_tract.jpg|thumb|280px|Caption 1]]
 |}

@@ Line 16: / Line 16: @@
 ===Authors, Collaborators & Contact===
-* Author1: Raul San Jose, BWH
+* Author1: Raúl San José Estépar, BWH
 * Contributor1: Alex Yarmakovich, Isomics
-* Contact: Raul San Jose, lmi.bwh.harvard.edu/~rjosest
+* Contact: http://lmi.bwh.harvard.edu/~rjosest/address.html]
 ===Module Description===

@@ Line 27: / Line 27: @@
 ===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 example by manually delineating the ROI using the Editor module. Second, the DWI has to be loaded and the tensor has to be created using the [http://www.slicer.org/slicerWiki/index.php/Modules:DiffusionTensorEstimation-Documentation-3.4 | Diffusion Tensor Estimation]. Thrid, start the ROI Seeding using the DTI volume and the ROI labelmap as main volume inputs.
+* We want to study the white matter integrate across a population for a given tract. ROISeeding can be used to carry this study.
 ===Quick Tour of Features and Use===

@@ Line 6: / Line 6: @@
 {|
 |[[Image:screenshotBlank.png|thumb|280px|Caption 1]]
 |}
@@ Line 13: / Line 11: @@
 ===Module Type & Category===
-Type: Interactive or CLI
+Type: CLI
 Category: Base or (Filtering, Registration, ''etc.'')
 ===Authors, Collaborators & Contact===
-* Author1: Affiliation & logo, if desired
+* Author1: Raul San Jose, BWH
-* Contributor1: Affiliation & logo, if desired
+* Contributor1: Alex Yarmakovich, Isomics
-* Contributor2: Affiliation & logo, if desired
+* Contact: Raul San Jose, lmi.bwh.harvard.edu/~rjosest
 ===Module Description===
-Overview of what the module does goes here.
+ROI 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.
 == Usage ==
@@ Line 30: / Line 27: @@
 ===Examples, Use Cases & Tutorials===
-* Note use cases for which this module is especially appropriate, and/or link to examples.
+* 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 example by manually delineating the ROI using the Editor module. Second, the DWI has to be loaded and the tensor has to be created using the [Diffusion Tensor Estimation | Modules:DiffusionTensorEstimation-Documentation-3.4]. Thrid, start the ROI Seeding using the DTI volume and the ROI labelmap as main volume inputs.
 ===Quick Tour of Features and Use===
-List all the panels in your interface, their features, what they mean, and how to use them. For instance:
+The module is very straighforward to use:
-* '''Input panel:'''
+* '''Input DTI volume:'''set the DTI volume that is going to be used for tractography
 * '''Parameters panel:'''
 * '''Output panel:'''
 * '''Viewing panel:'''
+=== Caveats and other limitations ===
-Should note somewhere that 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. But this is not immediately obvious..  -inorton
+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 | http://www.slicer.org/slicerWiki/index.php/Modules:ResampleVolume2-Documentation-3.4].
 == Development ==
@@ Line 49: / Line 44: @@
 ===Dependencies===
-Other modules or packages that are required for this module's use.
+None
 ===Known bugs===
 Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.