Documentation/4.4/gif tutorial - Revision history

Irosen: /* Tractography exploration of the ipsilateral and contralateral side */

2015-07-09T20:24:29Z

Tractography exploration of the ipsilateral and contralateral side

Irosen: /* Tractography exploration of the ipsilateral and contralateral side */

2015-07-09T20:23:00Z

Tractography exploration of the ipsilateral and contralateral side

Irosen: /* Tractography exploration of peritumoral white matter fibers */

2015-07-09T19:58:14Z

Tractography exploration of peritumoral white matter fibers

Irosen: /* Tractography */

2015-07-09T19:22:50Z

Tractography

Irosen: /* Tractography */

2015-07-09T18:36:35Z

Tractography

Irosen: /* Loading DTI and Baseline Data */

2015-07-09T18:32:24Z

Loading DTI and Baseline Data

Irosen at 18:18, 9 July 2015

2015-07-09T18:18:45Z

Irosen: /* Tractography */

2015-07-09T18:04:54Z

Tractography

Irosen: /* Tractography */

2015-07-09T18:04:05Z

Tractography

Irosen at 18:02, 9 July 2015

2015-07-09T18:02:59Z

@@ Line 79: / Line 79: @@
 in the 3D viewer.]]
 |- style="height: 100px;"
-|[[image:n.gif|600px|frame|3. Under the "Tractography Seeding Parameters set the Minimum Path Length to 10.0 mm and the FA Stopping Value at 0.15 ]]
+|[[image:n.gif|600px|frame|3. Under IO set Input DTI Volume to "DTIVolume", set Fiducial List or Model to "F", set Output Fiber Bundle to "Create new Fiber Bundle", then click ok for the pop-up. ]]
 |- style="height: 100px;"
-|[[image:o.gif|600px|frame|4. Under IO set Input DTI Volume to "DTIVolume", set Fiducial List or Model to "F", set Output Fiber Bundle to "Create new Fiber Bundle", then click ok for the pop-up.]]
+|[[image:o.gif|600px|frame|4. Under the "Tractography Seeding Parameters" set the Minimum Path Length to 10.0 mm and the FA Stopping Value at 0.15 ]]
 |- style="height: 100px;"
 |}
 </div>

@@ Line 73: / Line 73: @@
 <div style="width: 62%; height:525px; overflow:auto; border: 2px solid #088; margin: 1em auto 1em auto;">
 {|style="width: 62%; height: 200px;" border="1"
-|[[image:l.gif|600px|frame|1. Load the sample data by selecting "Load Data", then "Choose Directory to Add" and finally going to wherever it is that you downloaded the sample data and selecting the folder WhiteMatterExplorationData]]
+|[[image:l.gif|600px|frame|1. a) Click on the Modules menu and select the module
 |- style="height: 100px;"
-|[[image:m.gif|600px|frame|2. Click on the pin icon to display the slice menu,then click on the link icon to link the 3 anatomical viewers. Then change the background so it is set to BaselineVolume]]
+|[[image:m.gif|600px|frame|2. Select the Fiducial icon located at the top, and position the F-1 point next to the cystic part of the tumor by clicking near it
 |- style="height: 100px;"
-|[[image:n.gif|600px|frame|3. a) Click on the Layout Menu and select Red Slice Only. b) Select the Volumes Module from the Modules menu]]
+|[[image:n.gif|600px|frame|3. Under the "Tractography Seeding Parameters set the Minimum Path Length to 10.0 mm and the FA Stopping Value at 0.15 ]]
 |- style="height: 100px;"
-|[[image:o.gif|600px|frame|Manually adjust the Window Level editor presets with the Volume module menu]]
+|[[image:o.gif|600px|frame|4. Under IO set Input DTI Volume to "DTIVolume", set Fiducial List or Model to "F", set Output Fiber Bundle to "Create new Fiber Bundle", then click ok for the pop-up.]]
 |- style="height: 100px;"
 |}
 </div>

@@ Line 50: / Line 50: @@
 <div style="width: 62%; height:525px; overflow:auto; border: 2px solid #088; margin: 1em auto 1em auto;">
 {|style="width: 62%; height: 200px;" border="1"
-|[[image:x.gif|600px|frame|1. Load the sample data by selecting "Load Data", then "Choose Directory to Add" and finally going to wherever it is that you downloaded the sample data and selecting the folder WhiteMatterExplorationData]]
+|[[image:x.gif|600px|frame|1. a) Make sure the cystic part is selected and visible in the 3 slice views. b) Click on the Dilate Effect tool then click on the cystic part of the tumor on the red slice view.]]
 |- style="height: 100px;"
-|[[image:y.gif|600px|frame|2. Click on the pin icon to display the slice menu,then click on the link icon to link the 3 anatomical viewers. Then change the background so it is set to BaselineVolume]]
+|[[image:y.gif|600px|frame|2. Click on Apply 3 times to generate the peritumoral volume]]
 |- style="height: 100px;"
-|[[image:z.gif|600px|frame|3. a) Click on the Layout Menu and select Red Slice Only. b) Select the Volumes Module from the Modules menu]]
+|[[image:z.gif|600px|frame|3. Select the module "Tractography Label Map Seeding" by clicking "Editor" at the top, then "Diffusion", then "Diffusion Tensor Imaging".]]
 |- style="height: 100px;"
-|[[image:c.gif|600px|frame|Manually adjust the Window Level editor presets with the Volume module menu]]
+|[[image:c.gif|600px|frame|4. Make sure that "DTI Volume" is selected for Input DTI Volume and "BaselineVolumeregion_1-label" is selected for Input Label Map]]
 |- style="height: 100px;"
 {|style="width: 62%; height: 200px;" border="1"
-|[[image:a.gif|600px|frame|1. Load the sample data by selecting "Load Data", then "Choose Directory to Add" and finally going to wherever it is that you downloaded the sample data and selecting the folder WhiteMatterExplorationData]]
+|[[image:a.gif|600px|frame|5. a) For Output Fiber Bundle select "Create and
 |- style="height: 100px;"
-|[[image:b.gif|600px|frame|2. Click on the pin icon to display the slice menu,then click on the link icon to link the 3 anatomical viewers. Then change the background so it is set to BaselineVolume]]
+|[[image:b.gif|600px|frame|6. a) Under the Seed Placement Options: Check the Use Index Space. b) Under Tractography Seeding parameter set the stopping value to "0.15" and make sure for Stopping Criteria that "Fractional Anisotropy" is selected.  ]]
 |- style="height: 100px;"
-|[[image:d.gif|600px|frame|3. a) Click on the Layout Menu and select Red Slice Only. b) Select the Volumes Module from the Modules menu]]
+|[[image:d.gif|600px|frame|7. Under Label Definition set the "Seeding Label" to 293, and Click on Apply]]
 |- style="height: 100px;"
 |}

← Older revision		Revision as of 19:22, 9 July 2015
Line 46:		Line 46:


−	===Tractography===	+	===Tractography exploration of peritumoral white matter fibers===

	<div style="width: 62%; height:525px; overflow:auto; border: 2px solid #088; margin: 1em auto 1em auto;">		<div style="width: 62%; height:525px; overflow:auto; border: 2px solid #088; margin: 1em auto 1em auto;">

@@ Line 67: / Line 67: @@
 |}
 </div>
 ===Tractography exploration of the ipsilateral and contralateral side ===

← Older revision		Revision as of 18:32, 9 July 2015
Line 69:		Line 69:


−	===~~Loading DTI~~ and ~~Baseline Data~~===	+	===Tractography exploration of the ipsilateral and contralateral side ===

	<div style="width: 62%; height:525px; overflow:auto; border: 2px solid #088; margin: 1em auto 1em auto;">		<div style="width: 62%; height:525px; overflow:auto; border: 2px solid #088; margin: 1em auto 1em auto;">