Difference between revisions of "Slicer:Workshops:User Training 101"

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This is the introductory '''Slicer 2.6 ''' training material.
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[[Image:Nac.png|thumb|right|[http://nac.spl.harvard.edu Link to the '''NAC''' website]]]
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<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 =
 
= Introduction =
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This is a training compendium for using '''3D Slicer version 2'''. If you are looking for information about Slicer version 3, please follow this [https://www.slicer.org/wiki/Slicer3.6:Training#Software_tutorials Slicer3 101 page].
  
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You can begin to learn how to
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This work is jointly sponsored by NA-MIC, NAC and NCIGT.
  
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This series of courses will teach you how to
 
* load and view data
 
* load and view data
 
* segment data and create 3D models
 
* segment data and create 3D models
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* use the DTI and fMRI modules
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* perform Diffusion Tensor Imaging and fMRI analysis
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For an overview of Slicer, download this [[Media:NA-MIC-05-Slicer-Overview.ppt| slideshow]]
  
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For a high level description of 3D Slicer, download this [[Media:NA-MIC-05-Slicer-Overview.ppt| presentation]]
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= Software =
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<div class="floatleft"><span>[[Image:3DSlicer.png|80px|[[Image:3DSlicer.png| 3D Slicer Logo]]]]</span></div>
  
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= Software Installation =
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The current version of Slicer that is fully supported is Slicer 2.6.
  
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Before you can work through the tutorial materials you have to install the 3D slicer program and download the sample data sets and tutorials.  
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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.
  
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The Slicer software can be found in [[Slicer:Slicer2.6_Getting_Started|Slicer 2.6 Getting Started: Software & Sample Data ]].
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= Training Compendium =
  
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=Slicer 2 Materials=
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For course related questions, please send an e-mail to '''Sonia Pujol, Ph.D. (spujol at bwh.harvard.edu)'''.
  
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{| border="1"
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[[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).]]
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|- bgcolor="#ddffff"
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| '''Contents'''
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{| border="2" cellpadding="5"
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| '''Presentation'''
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|- bgcolor="white"
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| '''Data'''
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|  
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|- bgcolor="#ddffff"
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| '''Course'''
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| '''Slicer'''
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| '''Dataset'''
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|
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|- bgcolor="white"
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|
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||[[Image:Training1 LoadingViewing.PNG|50px]]
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|- bgcolor="#ddffff"
 
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| Loading and Viewing Data
 
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[[Media:SlicerTraining1LoadingAndViewingData.ppt|Slicer Training 1 ]]
 
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|
 
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[[Media:Tutorial-with-dicom.zip|Dataset Training 1]]
 
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|- bgcolor="#ddffff"
 
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| Manual Segmentation and Model Making
 
 
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|
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[[Media:Slicer_Segmentation_Tutorial.ppt|Slicer Training 2 ]]
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[[Media:SlicerTraining1LoadingAndViewingData.ppt| Data Loading and Visualization ]]
 
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|
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[[Media:Tutorial-with-dicom.zip|Dataset Training 2]]
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[[Media:Tutorial-with-dicom.zip|Tutorial_with_dicom.zip]]
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|- bgcolor="#ddffff"
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|- bgcolor="white"
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| Level-Set Segmentation
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| [[Image:Training7Save.PNG|50px]]
 
|
 
|
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[[Media:03-LevelSet.ppt|Slicer Training 3]]
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[[Media:SlicerTraining7SavingData.ppt| Data Saving ]]
 
|
 
|
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[[Media:Tutorial-with-dicom.zip|Dataset Training 3]]
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[[Media:Tutorial-with-dicom.zip|Tutorial-with-dicom.zip]]
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|- bgcolor="#ddffff"
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|- bgcolor="white"
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| Diffusion Tensor Imaging
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|[[Image:Training2Segmentation.PNG|50px]]
 
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|
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[[Media:Slicer_DTMRI_Training4.ppt| Slicer Training 4]]
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[[Media:Slicer_Segmentation_Tutorial.ppt| Manual Segmentation ]]
 
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|
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[[Media:SlicerSampleDTI.zip| Dataset Training 4.1]] [[Media:Dwi-dicom.zip|Dataset Training 4.2]]
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[[Media:Tutorial-with-dicom.zip|Tutorial_with_dicom.zip]]
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|- bgcolor="#ddffff"
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|- bgcolor="white"
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| Functional Magnetic Resonance Imaging
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|[[Image:Training3LevelSets.PNG|50px]]
 
|
 
|
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[[Media:SlicerTraining5_fMRI.ppt| Slicer Training 5]]
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[[Media:03-LevelSet.ppt|Level-Set Segmentation ]]
 
|
 
|
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[[Media:FMRIData1_short.zip|Dataset Training 5.1]] [[Media:FMRIData2_long.zip|Dataset Training 5.2]]
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[[Media:Tutorial-with-dicom.zip|Tutorial_with_dicom.zip]]
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|- bgcolor="#ddffff"
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|- bgcolor="white"
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| vtkFreeSurferReaders
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| [[Image:Training10EM.png|50px]]
 
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|
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[[Media:SlicerTraining6_vtkFreeSurferReaders.ppt| Slicer Training 6 ]]
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[[Media:SlicerAdvancedTraining_EMBrainAtlasClassifier_V1.0.ppt| Automatic Brain Segmentation ]]
 
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|
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[[Media:FreeSurferSubjects.zip|Dataset Training 6 ]]
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[[Media:BrainAtlasClassifier.zip|BrainAtlasClassifier.zip ]]
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|- bgcolor="#ddffff"
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|- bgcolor="white"
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| Saving Data
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| [[Image:Training11Registration.PNG|55px]]
 
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|
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[[Media:SlicerTraining7SavingData.ppt| Slicer Training 7]]
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[[Media:SlicerAdvancedTraining11_Registration.ppt| Registration]]
 
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[[Media:Tutorial-with-dicom.zip|Dataset Training 7]]
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[[Media:RegistrationSample.zip| RegistrationSample.zip]]
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|- bgcolor="#ddffff"
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|- bgcolor="white"
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| Nrrd File Format
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|[[Image:Training4DTI.PNG|50px]]
 
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|
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[[Media:SlicerTraining8-NrrdFileFormat.ppt| Slicer Training 8]]
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[[Media:Slicer_DTMRI_Training4.ppt| Diffusion Tensor Imaging Analysis ]]
 
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|
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[[Media:Tensor_data.zip|Dataset Training 8]]
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[[Media:SlicerSampleDTI.zip| SlicerSampleDTI.zip]] [[Media:Dwi-dicom.zip|Dwi-dicom.zip]]
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|- bgcolor="#ddffff"
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|- bgcolor="white"
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| Dicom to Nrrd Conversion
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| [[Image:Training8Nrrd.PNG|50px]]
 
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|
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[[Media:SlicerTraining9_DTI-FromDicomToNrrd.ppt| Slicer Training 9]]
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[[Media:SlicerTraining8-NrrdFileFormat.ppt| Nrrd File Format]]
 
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|
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[[Media:Dwi-dicom.zip|Dataset Training 9]]
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[[Media:Tensor_data.zip|Tensor_data.zip]]
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|- bgcolor="#ddffff"
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|- bgcolor="white"
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| EMBrainAtlasClassifier
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| [[Image:Training9DicomToNrrd.PNG|50px]]
 
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|
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[[Media:SlicerAdvancedTraining_EMBrainAtlasClassifier_V1.0.ppt| Slicer Training 10 ]]
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[[Media:SlicerTraining9_DTI-FromDicomToNrrd.ppt| Dicom to Nrrd Conversion ]]
 
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|
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[[Media:BrainAtlasClassifier.zip|Dataset Training 10 ]]
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[[Media:Dwi-dicom.zip|Dwi-dicom.zip]]
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|- bgcolor="#ddffff"
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|- bgcolor="white"
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| Registration
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| [[Image:Training5fMRI.PNG|50px]]
 
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|
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[[Media:SlicerAdvancedTraining11_Registration.ppt| Slicer Training 11]]
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[[Media:SlicerTraining5_fMRI.ppt| Functional Magnetic Resonace Imaging Analysis ]]
 
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|
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[[Media:RegistrationSample.zip|Dataset Training 11 ]]
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[[Media:FMRIData1_short.zip|FMRIData1_short.zip]] [[Media:FMRIData2_long.zip|FMRIData2_long.zip]]
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|- bgcolor="#ddffff"
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|- bgcolor="white"
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| fMRI Statistical Analysis
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| [[Image:Training6FreeSurfer.png|50px]]
 
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[http://ocw.mit.edu/OcwWeb/Health-Sciences-and-Technology/HST-583Fall-2004/CourseHome/ HST.583 Functional Magnetic Resonance Imaging]
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[[Media:SlicerTraining6_vtkFreeSurferReaders.ppt| FreeSurfer Reader ]]
 
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|
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[http://mgh-edu.nbirn.net/tutorial.html Tutorial documentation]
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[[Media:FreeSurferSubjects.zip|FreeSurferSubjects.zip ]]
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|
 
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<br />
 
 
|}
 
|}
  
 
= Slicer Additional Resources =
 
= Slicer Additional Resources =
 
[[Image:Limbic-2007.jpg|thumb|right|330px| A rendering of the Limbic System from the SPL PNL brain atlas]]
 
[[Image:Limbic-2007.jpg|thumb|right|330px| A rendering of the Limbic System from the SPL PNL brain atlas]]
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* [[BrainAtlas|SPL PNL Brain Atlas]]
 
* [[BrainAtlas|SPL PNL Brain Atlas]]
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* [[IGT-Tutorials|IGT Tutorial Materials]]
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* [[Media:Training_EMLocalSegment_v1.pdf | EMSegmenter]] for multi-channel [[Media:EMSegmentTutorial.zip|data]] and white matter hyperintensities
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* [[Media:Training_EMLocalSegment_v1.pdf | EMSegmenter]] for multi-channel data and white matter hyperintensities
 
 
* [[DataFusion|Data Fusion and Registration]]
 
* [[DataFusion|Data Fusion and Registration]]
 
* [http://astromed.iic.harvard.edu/UsingSlicer Using 3DSlicer in Astronomy]
 
* [http://astromed.iic.harvard.edu/UsingSlicer Using 3DSlicer in Astronomy]
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* [[SlicerOnBIRN|How to use Slicer with BIRN]]
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* [https://www.slicer.org/wiki/SlicerOnBIRN How to use Slicer with BIRN]
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* [[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.
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* 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
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* [http://www.airwayinspector.org/ Airway inspector]: 3D Slicer based tool for morphometry analysis of the lung airways and emphysema.
  
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= Feedback and Bug reports =
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= Feedback =
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[[Image:101.png|thumb|left|250px|Excerpts from the Slicer 101 courses: Diffusion Tensor Imaging fiber tractography (top); fMRI activation map (lower-left); automatic brain segmentation (lower-right).]]
 
  
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* [http://www.slicer.org/pages/Slicer_Community Feedback about Slicer]
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* [[Slicer:Feedback|Feedback about Slicer]]
 
 
* [http://www.na-mic.org/Bug/ Bug reports]
 
* [http://www.na-mic.org/Bug/ Bug reports]
  
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<br /> Back to [[Training:Main|Training:Main]]
 
<br /> Back to [[Training:Main|Training:Main]]
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[[Category:Slicer]]

Latest revision as of 18:07, 10 July 2017

Home < Slicer:Workshops:User Training 101
Link to the NAC website

Introduction

This is a training compendium for using 3D Slicer version 2. If you are looking for information about Slicer version 3, please follow this Slicer3 101 page.

This work is jointly sponsored by NA-MIC, NAC and NCIGT.

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, download this slideshow

Software

The current version of Slicer that is fully supported is Slicer 2.6.

Please follow the 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).

Excerpts from the Slicer 101 courses: Diffusion Tensor Imaging fiber tractography (top); fMRI activation map (lower-left); automatic brain segmentation (lower-right).
Course Dataset
Training1 LoadingViewing.PNG

Data Loading and Visualization

Tutorial_with_dicom.zip

Training7Save.PNG

Data Saving

Tutorial-with-dicom.zip

Training2Segmentation.PNG

Manual Segmentation

Tutorial_with_dicom.zip

Training3LevelSets.PNG

Level-Set Segmentation

Tutorial_with_dicom.zip

Training10EM.png

Automatic Brain Segmentation

BrainAtlasClassifier.zip

Training11Registration.PNG

Registration

RegistrationSample.zip

Training4DTI.PNG

Diffusion Tensor Imaging Analysis

SlicerSampleDTI.zip Dwi-dicom.zip

Training8Nrrd.PNG

Nrrd File Format

Tensor_data.zip

Training9DicomToNrrd.PNG

Dicom to Nrrd Conversion

Dwi-dicom.zip

Training5fMRI.PNG

Functional Magnetic Resonace Imaging Analysis

FMRIData1_short.zip FMRIData2_long.zip

Training6FreeSurfer.png

FreeSurfer Reader

FreeSurferSubjects.zip

Slicer Additional Resources

A rendering of the Limbic System from the SPL PNL brain atlas

Feedback

Acknowledgements

  • Slicer is being developed by a community of contributors. For more information see the Slicer website.


Back to Training:Main

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