Modules:Volumes:Diffusion Editor-Documentation - Revision history

Grundlett: Text replacement - "https?:\/\/www.slicer.org\/slicerWiki\/index.php\/([^ ]+) " to "https://www.slicer.org/wiki/$1"

2019-11-27T14:52:17Z

Text replacement - "https?:\/\/www.slicer.org\/slicerWiki\/index.php\/([^ ]+) " to "https://www.slicer.org/wiki/$1"

Grundlett: Text replacement - "https?:\/\/(?:www|wiki)\.slicer\.org\/slicerWiki\/index\.php\/([^ ]+) " to "https://www.slicer.org/wiki/$1 "

2019-11-27T13:16:04Z

Text replacement - "https?:\/\/(?:www|wiki)\.slicer\.org\/slicerWiki\/index\.php\/([^ ]+) " to "https://www.slicer.org/wiki/$1 "

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

2019-11-27T02:21:21Z

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

Lasso: /* Known issues / bugs */

2017-04-12T20:52:59Z

Known issues / bugs

Kikinis: /* References */

2008-09-21T13:52:17Z

References

Kerstin: /* References */

2008-09-21T10:16:16Z

References

Kerstin: /* Tutorials */

2008-07-18T15:55:54Z

Tutorials

Kerstin: /* Module Description */

2008-07-18T15:55:26Z

Module Description

Kerstin: /* Used Tensor Estimation */

2008-07-13T13:45:14Z

Used Tensor Estimation

Kerstin: /* Used Tractography Fiducial Seeding */

2008-07-13T13:44:37Z

Used Tractography Fiducial Seeding

@@ Line 43: / Line 43: @@
 The Diffusion Editor uses the Tractography Fiducial Seeding module of Slicer to compute tracts.
 * The Diffusion Editor uses the default parameters. To change tractography parameters select the modul: Tractography/Seeding/Fiducial Seeding [[Slicer3:DTMRI#Tractography_Fiducial_Seeding_Module].|Changes there have an immediate impact for the tracts in the Diffusion Editor.
-* For more detailed exploring of tracts use the Fiducial Seeding module or for display options select the module Tractography/DisplayLoadSave [http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI#Tractography_Module]].
+* For more detailed exploring of tracts use the Fiducial Seeding module or for display options select the module Tractography/DisplayLoadSave [https://www.slicer.org/wiki/Slicer3:DTMRI#Tractography_Module]].* See [[Slicer3:DTMRI#Tractography_Module|here]] for more information on the Tractography modules.
 === Current features of the Diffusion Editor===

@@ Line 171: / Line 171: @@
 ==References==
-Thesis: [[Image:Thesis_letter.pdf|http://www.slicer.org/slicerWiki/index.php/Media:Thesis_letter.pdf]]
+Thesis: [[Image:Thesis_letter.pdf|https://www.slicer.org/wiki/Media:Thesis_letter.pdf]] DTMRI: [[Slicer3:DTMRI|https://www.slicer.org/wiki/Slicer3:DTMRI]] Nrrd format: [http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:Nrrd_format http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:Nrrd_format]
 DICOM for DWI and DTI : [http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI]

@@ Line 34: / Line 34: @@
 The Diffusion Editor uses the Tensor Estimation CLM (Command Line Module) of Slicer to compute tensors.
 * The module provides the linear-least-squares, non-linear-least squares and weighted-least-square method for the estimation. But the DiffusionEditor uses the linear-least-squares method by default, as it is the fastest and most robust.
-* See [http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI#Tensor_Estimation_from_DWI_Module], [http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:TeemExamples#tend_estim:_tensor_estimation] for more information on the Tensor Estimation CLM.
+* See [[Slicer3:DTMRI#Tensor_Estimation_from_DWI_Module],|[http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:TeemExamples#tend_estim:_tensor_estimation]] for more information on the Tensor Estimation CLM.
 The testing frame provides just a small subset of DTI display options. For more detailed settings
@@ Line 42: / Line 42: @@
 === Used Tractography Fiducial Seeding ===
 The Diffusion Editor uses the Tractography Fiducial Seeding module of Slicer to compute tracts.
-* The Diffusion Editor uses the default parameters. To change tractography parameters select the modul: Tractography/Seeding/Fiducial Seeding [http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI#Tractography_Fiducial_Seeding_Module]. Changes there have an immediate impact for the tracts in the Diffusion Editor.
+* The Diffusion Editor uses the default parameters. To change tractography parameters select the modul: Tractography/Seeding/Fiducial Seeding [[Slicer3:DTMRI#Tractography_Fiducial_Seeding_Module].|Changes there have an immediate impact for the tracts in the Diffusion Editor.
-* For more detailed exploring of tracts use the Fiducial Seeding module or for display options select the module Tractography/DisplayLoadSave [http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI#Tractography_Module].
+* For more detailed exploring of tracts use the Fiducial Seeding module or for display options select the module Tractography/DisplayLoadSave [http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI#Tractography_Module]].
-* See [http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI#Tractography_Module here] for more information on the Tractography modules.
+* See [[Slicer3:DTMRI#Tractography_Module|here]] for more information on the Tractography modules.
 === Current features of the Diffusion Editor===
@@ Line 140: / Line 140: @@
 ** Future work: Adding different views of gradients/bValues.
 * Checking gradients when one types new values in the textbox is slowly. Reason: SetDiffusionGradients of the vtkMRMLDiffusionWeightedVolumeNode seems to trigger many events.
-** Future work: Use [http://www.slicer.org/slicerWiki/index.php/Slicer3:EventBroker Eventbroker] for performance analysis and if necessary turn off events.
+** Future work: Use [[Slicer3:EventBroker|Eventbroker]] for performance analysis and if necessary turn off events.
 == Source code & documentation ==
@@ Line 171: / Line 171: @@
 ==References==
-Thesis: [http://www.slicer.org/slicerWiki/index.php/Image:Thesis_letter.pdf http://www.slicer.org/slicerWiki/index.php/Media:Thesis_letter.pdf]
+Thesis: [[Image:Thesis_letter.pdf|http://www.slicer.org/slicerWiki/index.php/Media:Thesis_letter.pdf]]
-DTMRI: [http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI]
+DTMRI: [[Slicer3:DTMRI|http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI]]
 Nrrd format: [http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:Nrrd_format http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:Nrrd_format]
 DICOM for DWI and DTI : [http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI http://wiki.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI]

@@ Line 132: / Line 132: @@
 http://na-mic.org/Mantis/main_page.php
-Queries, feature requests and other feedback should be directed to slicer-devel |at| bwh.harvard.edu. You can also sign up for Slicers user and developer list to make sure you hear of new developments, releases and bug fixes.
+Queries, feature requests and other feedback should be posted on [https://discourse.slicer.org/ Slicer discourse website]. You can also sign up at the website to make sure you hear of new developments, releases and bug fixes.
 === Issues ===

@@ Line 171: / Line 171: @@
 ==References==
-Thesis: [http://www.slicer.org/slicerWiki/index.php/Image:Thesis_letter.pdf http://www.slicer.org/slicerWiki/index.php/Image:Thesis_letter.pdf]
+Thesis: [http://www.slicer.org/slicerWiki/index.php/Image:Thesis_letter.pdf http://www.slicer.org/slicerWiki/index.php/Media:Thesis_letter.pdf]
 DTMRI: [http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI http://www.slicer.org/slicerWiki/index.php/Slicer3:DTMRI]

@@ Line 71: / Line 71: @@
 ! title !!short description
 |-
-| [[Tutorials:DiffusionEditor-Load DWI-Dicom| Load]]  ||Load a DWI dicom data set in Slicer.
+| [[Tutorials:DiffusionEditor-Load DWI-Dicom| Load DICOM]]  ||Load a DWI dicom data set in Slicer.
 |-
-| [[Tutorials:DiffusionEditor-Edit Gradients | Gradients ]]||Change gradients manually and load them from a file. Save your changes afterwards.
+| [[Tutorials:DiffusionEditor-Edit Gradients | Edit gradients ]]||Change gradients manually and load them from a file. Save your changes afterwards.
 |-
-| [[Tutorials:DiffusionEditor-Edit Measurement frame| Measurement frame]] ||Change the measurement frame by swapping and inverting. Save your changes afterwards.
+| [[Tutorials:DiffusionEditor-Edit Measurement frame| Edit measurement frame]] ||Change the measurement frame by swapping and inverting. Save your changes afterwards.
 |-
 | [[Tutorials:DiffusionEditor-Testing | Testing ]]||Run tensor estimation and show glyphs and tracts;

@@ Line 24: / Line 24: @@
 As the documentation of acquisition parameters in dicom data is not standardized, MRI scanners (Siemens, GE) handle gradients/bValues/measurement frame differently in their dicom headers. Because of that there is a big need to add/modify them manually.
-The Diffusion Editor is a 3D Slicer module that allows modifying parameters (gradients, bValues, measurement frame) of DWI data and provides a quick way to interpret them. For that it estimates a tensor and shows glyphs and tracts for visual exploration.
+The Diffusion Editor is a 3D Slicer module, which allows modifying parameters (gradients, bValues, measurement frame) of DWI data and provides a quick way to interpret them. For that it estimates a tensor and shows glyphs and tracts for visual exploration.
 === Measurement Frame ===