Slicer:Workshops:User Training 101 SPujol - Revision history

Grundlett: Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

2017-07-10T18:07:31Z

Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

Melonakos at 20:55, 6 November 2008

2008-11-06T20:55:05Z

Melonakos at 19:35, 6 November 2008

2008-11-06T19:35:54Z

Melonakos at 18:10, 6 November 2008

2008-11-06T18:10:43Z

Spujol at 16:43, 1 June 2007

2007-06-01T16:43:25Z

Spujol at 12:24, 31 May 2007

2007-05-31T12:24:38Z

Spujol at 10:39, 22 May 2007

2007-05-22T10:39:26Z

Spujol at 09:17, 22 May 2007

2007-05-22T09:17:25Z

New page

<div class="thumb tright"><div style="width: 96px">[[Image:Nac.png|[[Image:Nac.png|Link to the NAC website]]]]<div class="thumbcaption">[http://www.spl.harvard.edu/nac Link to the NAC website]</div></div></div>

= Introduction =
This is a training compendium for neuroimage analysis using Slicer2.6.
You can begin to learn how to
* load and view data
* segment data and create 3D models
* perform Diffusion Tensor Imaging and fMRI analysis
For an overview, dowload this [[Media:NA-MIC-05-Slicer-Overview.ppt| slideshow]]

= Training Compendium =
For course related questions, please send an e-mail to Sonia Pujol, Ph.D. (spujol at bwh.harvard.edu).
[[Image:101.png|thumb|right|350px|Excerpts from the Slicer 101 courses: Diffusion Tensor Imaging fiber tractography (top); fMRI activation map (lower-left); automatic brain segmentation (lot).]]
* Training 1: [[Media:SlicerTraining1LoadingAndViewingData.ppt| Loading and Viewing Data ]]
* Training 2: [[Media:Slicer_Segmentation_Tutorial.ppt|Manual Segmentation and Model Making ]]
* Training 3: [[Media:03-LevelSet.ppt|Level-Set Segmentation ]]
* Training 4: [[Media:Slicer_DTMRI_Training4.ppt|Diffusion Tensor Imaging Analysis ]]
* Training 5: [[Media:SlicerTraining5_fMRI.ppt| Functional Magnetic Resonance Imaging Analysis ]]
* Training 6: [[Media:SlicerTraining6_vtkFreeSurferReaders.ppt| FreeSurferReader ]]
* Training 7: [[Media:SlicerTraining7SavingData.ppt|Volume, Model and Scene Saving ]]
* Training 8: [[Media:SlicerTraining8-NrrdFileFormat.ppt|Nrrd File Format]]
* Training 9: [[Media:SlicerTraining9_DTI-FromDicomToNrrd.ppt|Dicom to Nrrd Conversion]]
* Advanced Training 10: [[Media:SlicerAdvancedTraining_EMBrainAtlasClassifier_V1.0.ppt|Automatic Segmentation of Brain Structures ]]
* Advanced Training 11: [[Media:SlicerAdvancedTraining11_Registration.ppt|Registration ]]

= Training Datasets =
* Get these data for Training 1,2,3: [[Media:Tutorial-with-dicom.zip|tutorial_with_dicom.zip]]
* Get these data for Training 4: [[Media:SlicerSampleDTI.zip|SlicerSampleDTI.zip ]] [[Media:Dwi-dicom.zip|dwi-dicom.zip]]
* Get these data for Training 5: [[Media:FMRIData1_short.zip|fMRIData_short.zip]], [[Media:FMRIData2_long.zip|fMRIData_long.zip]]
* Get these data for Training 6: [[Media:FreeSurferSubjects.zip|FreeSurferSubjects.zip ]]
* Get these data for Training 7: [[Media:Tutorial-with-dicom.zip|tutorial_with_dicom.zip]]
* Get these data for Training 8: [[Media:Tensor_data.zip| TensorData.zip]]
* Get these data for Training 9: [[Media:Dwi-dicom.zip|dwi-dicom.zip]]
* Get these data for Training 10: [[Media:BrainAtlasClassifier.zip|BrainAtlasClassifier.zip]]
* Get these data for Training 11: [[Media:RegistrationSample.zip|RegistrationSample.zip]]
* Get these extra set of interoperative data [[Media:Mrt-images.zip| mrt-images.zip]]
* Get these data for EMSegmenter demonstrations: [[Media:EMSegmentTutorial.zip|EMSegmentTutorial.zip]]

= Software Installation =

Please follow the [[Slicer:Slicer2.6_Getting_Started|Slicer 2.6 Getting Started]] instructions to install the current version of the Slicer program appropriate to your platform.

= Slicer Additional Resources =
[[Image:Limbic-2007.jpg|thumb|right|330px| A rendering of the Limbic System from the SPL PNL brain atlas]]

* [[BrainAtlas|SPL PNL Brain Atlas]]
* [[IGT-Tutorials|IGT Tutorial Materials]]
* [[Media:Training_EMLocalSegment_v1.pdf | EMSegmenter]] for multi-channel data and white matter hyperintensities
* [[DataFusion|Data Fusion and Registration]]
* [http://astromed.iic.harvard.edu/UsingSlicer Using 3DSlicer in Astronomy]
* [[SlicerOnBIRN|How to use Slicer with BIRN]]
* [[media:Abdomen.zip|CT based atlas of the abdomen]]. This data is organized in analogy to the brain atlas above. The zip archive contains a .txt file with the key for the label values and their anatomical meaning.

= Feedback and Bug reports =

* [[Slicer:Feedback|Feedback about Slicer]]
* [http://www.na-mic.org/Bug/ Bug reports]

= Acknowledgements =
*Slicer is being developed by a community of contributors. For more information see the [http://www.slicer.org Slicer] website.

<br /> Back to [[Training:Main|Training:Main]]

@@ Line 16: / Line 16: @@
 The current version of Slicer that is fully supported is Slicer 2.6.
-Please follow the [http://www.slicer.org/slicerWiki/index.php/Slicer:Slicer2.6_Getting_Started Slicer 2.6 Getting Started] instructions to install the version of the Slicer program appropriate to your platform.
+Please follow the [https://www.slicer.org/wiki/Slicer:Slicer2.6_Getting_Started Slicer 2.6 Getting Started] instructions to install the version of the Slicer program appropriate to your platform.
@@ Line 110: / Line 110: @@
 * [[DataFusion|Data Fusion and Registration]]
 * [http://astromed.iic.harvard.edu/UsingSlicer Using 3DSlicer in Astronomy]
-* [http://www.slicer.org/slicerWiki/index.php/SlicerOnBIRN How to use Slicer with BIRN]
+* [https://www.slicer.org/wiki/SlicerOnBIRN How to use Slicer with BIRN]
 * [[media:Abdomen.zip|CT based atlas of the abdomen]]. This data is organized in analogy to the brain atlas above. The zip archive contains a .txt file with the key for the label values and their anatomical meaning.

@@ Line 115: / Line 115: @@
 = Feedback  =
-* [[Slicer:Feedback|Feedback about Slicer]]
+* [http://www.slicer.org/pages/Slicer_Community Feedback about Slicer]
 * [http://www.na-mic.org/Bug/ Bug reports]

← Older revision		Revision as of 19:35, 6 November 2008
Line 16:		Line 16:
	The current version of Slicer that is fully supported is Slicer 2.6.		The current version of Slicer that is fully supported is Slicer 2.6.

−	Please follow the [[Slicer:Slicer2.6_Getting_Started\|Slicer 2.6 Getting Started]] instructions to install the version of the Slicer program appropriate to your platform.	+	Please follow the [http://www.slicer.org/slicerWiki/index.php/Slicer:Slicer2.6_Getting_Started Slicer 2.6 Getting Started] instructions to install the version of the Slicer program appropriate to your platform.

@@ Line 38: / Line 38: @@
+|
 [[Media:Tutorial-with-dicom.zip|Tutorial_with_dicom.zip]]
 |- bgcolor="white"
 |[[Image:Training2Segmentation.PNG|50px]]
@@ Line 92: / Line 98: @@
+|
 [[Media:FreeSurferSubjects.zip|FreeSurferSubjects.zip ]]
 |}

@@ Line 1: / Line 1: @@
-<div class="thumb tright"><div style="width: 96px">[[Image:Nac.png|[[Image:Nac.png|Link to the NAC website]]]]<div class="thumbcaption">[http://www.spl.harvard.edu/nac Link to the NAC website]</div></div></div>
+<div class="thumb tright"><div style="width: 90px">[[Image:Nac.png|[[Image:Nac.png|Link to the NAC website]]]]<div
 = Introduction =
-This is a training compendium for neuroimage analysis using Slicer2.6.
+This is a training compendium for neuroimage analysis using 3DSlicer.
-This series of course will teach you how to
 * load and view data
 * segment data and create 3D models
 * perform Diffusion Tensor Imaging and fMRI analysis
-For an overview, dowload this [[Media:NA-MIC-05-Slicer-Overview.ppt| slideshow]]
+For an overview of Slicer, dowload this [[Media:NA-MIC-05-Slicer-Overview.ppt| slideshow]]
 = Training Compendium =
 For course related questions, please send an e-mail to Sonia Pujol, Ph.D. (spujol at bwh.harvard.edu).
-= Training Material =
+[[Image:101.png|thumb|right|450px|Excerpts from the Slicer 101 courses: Diffusion Tensor Imaging fiber tractography (top); fMRI activation map (lower-left); automatic brain segmentation (lower-right).]]
-== Software Tool==
-Please follow the [[Slicer:Slicer2.6_Getting_Started|Slicer 2.6 Getting Started]] instructions to install the current version of the Slicer program appropriate to your platform.
+{| border="2"
-== Training Datasets ==
+|- bgcolor="white"
-* Get these data for Training 1,2,3: [[Media:Tutorial-with-dicom.zip|tutorial_with_dicom.zip]]
+| ''''''
-* Get these data for Training 4: [[Media:SlicerSampleDTI.zip|SlicerSampleDTI.zip ]] [[Media:Dwi-dicom.zip|dwi-dicom.zip]]
+| '''Course'''
-* Get these data for Training 5: [[Media:FMRIData1_short.zip|fMRIData_short.zip]], [[Media:FMRIData2_long.zip|fMRIData_long.zip]]
+| '''Dataset'''
-* Get these data for Training 6: [[Media:FreeSurferSubjects.zip|FreeSurferSubjects.zip ]]
+|- bgcolor="white"
-* Get these data for Training 7: [[Media:Tutorial-with-dicom.zip|tutorial_with_dicom.zip]]
+||[[Image:Training1 LoadingViewing.PNG|50px]]
-* Get these data for Training 8: [[Media:Tensor_data.zip| TensorData.zip]]
-* Get these data for Training 9: [[Media:Dwi-dicom.zip|dwi-dicom.zip]]
+[[Media:SlicerTraining1LoadingAndViewingData.ppt| Data Loading and Visualization ]]
-* Get these data for Training 10: [[Media:BrainAtlasClassifier.zip|BrainAtlasClassifier.zip]]
-* Get these data for Training 11: [[Media:RegistrationSample.zip|RegistrationSample.zip]]
+[[Media:Tutorial-with-dicom.zip|Tutorial_with_dicom.zip]]
-* Get these extra set of interoperative data [[Media:Mrt-images.zip| mrt-images.zip]]
+|- bgcolor="white"
-* Get these data for EMSegmenter demonstrations: [[Media:EMSegmentTutorial.zip|EMSegmentTutorial.zip]]
+|[[Image:Training2Segmentation.PNG|50px]]
 = Slicer Additional Resources =
@@ Line 45: / Line 108: @@
 * [[BrainAtlas|SPL PNL Brain Atlas]]
 * [[IGT-Tutorials|IGT Tutorial Materials]]
-* [[Media:Training_EMLocalSegment_v1.pdf | EMSegmenter]] for multi-channel data and white matter hyperintensities
+* [[Media:Training_EMLocalSegment_v1.pdf | EMSegmenter]] for multi-channel [[Media:EMSegmentTutorial.zip|data]] and white matter hyperintensities
 * [[DataFusion|Data Fusion and Registration]]
 * [http://astromed.iic.harvard.edu/UsingSlicer Using 3DSlicer in Astronomy]
@@ Line 51: / Line 114: @@
 * [[media:Abdomen.zip|CT based atlas of the abdomen]]. This data is organized in analogy to the brain atlas above. The zip archive contains a .txt file with the key for the label values and their anatomical meaning.
-= Feedback and Bug reports =
+= Feedback  =
 * [[Slicer:Feedback|Feedback about Slicer]]