Slicer:Workshops:User Training 101 SPujol - Revision history

Marianna at 14:20, 4 May 2011

2011-05-04T14:20:00Z

Marianna: 1 revision

2008-05-15T18:52:26Z

1 revision

Spujol at 16:43, 1 June 2007

2007-06-01T16:43:25Z

New page

<div class="thumb tright"><div style="width: 90px">[[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 3DSlicer.

This series of courses 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 of Slicer, dowload this [[Media:NA-MIC-05-Slicer-Overview.ppt| slideshow]]

= Software =
<div class="floatleft"><span>[[Image:3DSlicer.png|80px|[[Image:3DSlicer.png| 3D Slicer Logo]]]]</span></div>

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.

= 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|450px|Excerpts from the Slicer 101 courses: Diffusion Tensor Imaging fiber tractography (top); fMRI activation map (lower-left); automatic brain segmentation (lower-right).]]

{| border="2"
|- bgcolor="white"
| ''''''
| '''Course'''
| '''Dataset'''
|- bgcolor="white"
||[[Image:Training1 LoadingViewing.PNG|50px]]
|
[[Media:SlicerTraining1LoadingAndViewingData.ppt| Data Loading and Visualization ]]
|
[[Media:Tutorial-with-dicom.zip|Tutorial_with_dicom.zip]]
|- bgcolor="white"
| [[Image:Training7Save.PNG|50px]]
|
[[Media:SlicerTraining7SavingData.ppt| Data Saving ]]
|
[[Media:Tutorial-with-dicom.zip|Tutorial-with-dicom.zip]]
|- bgcolor="white"
|[[Image:Training2Segmentation.PNG|50px]]
|
[[Media:Slicer_Segmentation_Tutorial.ppt| Manual Segmentation ]]
|
[[Media:Tutorial-with-dicom.zip|Tutorial_with_dicom.zip]]
|- bgcolor="white"
|[[Image:Training3LevelSets.PNG|50px]]
|
[[Media:03-LevelSet.ppt|Level-Set Segmentation ]]
|
[[Media:Tutorial-with-dicom.zip|Tutorial_with_dicom.zip]]
|- bgcolor="white"
| [[Image:Training10EM.png|50px]]
|
[[Media:SlicerAdvancedTraining_EMBrainAtlasClassifier_V1.0.ppt| Automatic Brain Segmentation ]]
|
[[Media:BrainAtlasClassifier.zip|BrainAtlasClassifier.zip ]]
|- bgcolor="white"
| [[Image:Training11Registration.PNG|55px]]
|
[[Media:SlicerAdvancedTraining11_Registration.ppt| Registration]]
|
[[Media:RegistrationSample.zip| RegistrationSample.zip]]
|- bgcolor="white"
|[[Image:Training4DTI.PNG|50px]]
|
[[Media:Slicer_DTMRI_Training4.ppt| Diffusion Tensor Imaging Analysis ]]
|
[[Media:SlicerSampleDTI.zip| SlicerSampleDTI.zip]] [[Media:Dwi-dicom.zip|Dwi-dicom.zip]]
|- bgcolor="white"
| [[Image:Training8Nrrd.PNG|50px]]
|
[[Media:SlicerTraining8-NrrdFileFormat.ppt| Nrrd File Format]]
|
[[Media:Tensor_data.zip|Tensor_data.zip]]
|- bgcolor="white"
| [[Image:Training9DicomToNrrd.PNG|50px]]
|
[[Media:SlicerTraining9_DTI-FromDicomToNrrd.ppt| Nrrd to Dicom Conversion ]]
|
[[Media:Dwi-dicom.zip|Dwi-dicom.zip]]
|- bgcolor="white"
| [[Image:Training5fMRI.PNG|50px]]
|
[[Media:SlicerTraining5_fMRI.ppt| Functional Magnetic Resonace Imaging Analysis ]]
|
[[Media:FMRIData1_short.zip|FMRIData1_short.zip]] [[Media:FMRIData2_long.zip|FMRIData2_long.zip]]
|- bgcolor="white"
| [[Image:Training6FreeSurfer.PNG|50px]]
|
[[Media:SlicerTraining6_vtkFreeSurferReaders.ppt| FreeSurfer Reader ]]
|
[[Media:FreeSurferSubjects.zip|FreeSurferSubjects.zip ]]
|}

= 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 [[Media:EMSegmentTutorial.zip|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 =

* [[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 1: / Line 1: @@
-<div class="thumb tright"><div style="width: 90px">[[Image:Nac.png|[[Image:Nac.png|Link to the NAC website]]]]<div
+[[Image:Nac.png|thumb|right|[http://nac.spl.harvard.edu Link to the '''NAC''' website]]]
 = Introduction =
-This is a training compendium for neuroimage analysis using 3DSlicer.
+This is a training compendium for using 3DSlicer. This work is jointly sponsored by NA-MIC, NAC and NCIGT.
 This series of courses will teach you how to
@@ Line 9: / Line 7: @@
 * segment data and create 3D models
 * perform Diffusion Tensor Imaging and fMRI analysis
-For an overview of Slicer, 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]].
 = Software =
@@ Line 20: / Line 18: @@
 = Training Compendium =
@@ Line 29: / Line 28: @@
 {| border="2"
 |- bgcolor="white"
-| ''''''
 | '''Course'''
 | '''Dataset'''
@@ Line 63: / Line 62: @@
 [[Media:BrainAtlasClassifier.zip|BrainAtlasClassifier.zip ]]
 |- bgcolor="white"
-| [[Image:Training11Registration.PNG|55px]]
+| [[Image:Training11Registration.PNG|50px]]
+|
 [[Media:SlicerAdvancedTraining11_Registration.ppt| Registration]]
@@ Line 83: / Line 82: @@
 | [[Image:Training9DicomToNrrd.PNG|50px]]
+|
-[[Media:SlicerTraining9_DTI-FromDicomToNrrd.ppt| Nrrd to Dicom Conversion ]]
+[[Media:SlicerTraining9_DTI-FromDicomToNrrd.ppt| Dicom to Nrrd Conversion ]]
+|
 [[Media:Dwi-dicom.zip|Dwi-dicom.zip]]
@@ Line 93: / Line 92: @@
 [[Media:FMRIData1_short.zip|FMRIData1_short.zip]] [[Media:FMRIData2_long.zip|FMRIData2_long.zip]]
 |- bgcolor="white"
-| [[Image:Training6FreeSurfer.PNG|50px]]
+| [[Image:Training6FreeSurfer.png|50px]]
+|
 [[Media:SlicerTraining6_vtkFreeSurferReaders.ppt| FreeSurfer Reader ]]
@@ Line 99: / Line 98: @@
 [[Media:FreeSurferSubjects.zip|FreeSurferSubjects.zip ]]
 |}
 = 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]]
+* [http://www.slicer.org/publications/item/view/1265 SPL PNL Brain Atlas]
 * [[Media:Training_EMLocalSegment_v1.pdf | EMSegmenter]] for multi-channel [[Media:EMSegmentTutorial.zip|data]] and white matter hyperintensities
-* [[DataFusion|Data Fusion and Registration]]
+* [http://www.na-mic.org/Wiki/index.php/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.
+* CT based atlas of the [http://spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1266  abdomen] for Slicer 3. The [[media:Abdominal_Atlas_Tutorial08.ppt|tutorial]] describing how to load and display the data in Slicer 3
 = Feedback  =
@@ Line 120: / Line 117: @@
 = Acknowledgements =
 *Slicer is being developed by a community of contributors. For more information see the [http://www.slicer.org Slicer] website.

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