Difference between revisions of "Slicer:Workshops:User Training 101"
From NAMIC Wiki
| Line 1: | Line 1: | ||
| − | This is the introductory '''Slicer 2.6 ''' | + | This is the introductory '''Slicer 2.6 ''' training material. |
<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: 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> | ||
| Line 7: | Line 7: | ||
You can begin to learn how to | You can begin to learn how to | ||
| − | + | * load and view data | |
| − | + | * segment data and create 3D models | |
| − | + | * use the DTI and fMRI modules | |
| − | + | ||
| + | For an overview, dowload this [[Media:NA-MIC-05-Slicer-Overview.ppt| slideshow]] | ||
= Software Installation = | = Software Installation = | ||
| − | Please install the following software applications and files from the NAMIC site before the course: the current version of the Slicer program appropriate to your platform, the tutorial guide for Slicer, the generic sample data set. | + | Please install the following software applications and files from the NAMIC site before the course: the current version of the Slicer program appropriate to your platform, the tutorial guide for Slicer, the generic sample data set. This material is located in [[Slicer:Slicer2.6_Getting_Started|Slicer 2.6 Getting Started: Software & Sample Data ]]. |
| − | |||
| − | This material is located in [[Slicer:Slicer2.6_Getting_Started|Slicer 2.6 Getting Started: Software & Sample Data ]]. | ||
= Data to Download = | = Data to Download = | ||
| − | + | * Get the tutorial data with Dicom [[Media:Tutorial-with-dicom.zip|tutorial_with_dicom.zip]] | |
| − | + | * Get this extra set of interoperative data [[Media:Mrt-images.zip| mrt-images.zip]] | |
| − | + | * Get this data for testing registrations [[Media:Reg-sample.zip|reg-sample.zip]] | |
| − | + | * Get these data for DTI demonstrations: [[Media:SlicerSampleDTI.zip|SlicerSampleDTI.zip ]] [[Media:Dwi-dicom.zip|dwi-dicom.zip]] | |
| − | + | * Get these data for FreeSurfer demonstrations: [[Media:FreeSurferSubjects.zip|FreeSurferSubjects.zip ]] | |
| − | + | * Get these data for EMAtlasBrainClassifier demonstrations: [[Media:BrainAtlasClassifier.zip|BrainAtlasClassifier.zip]] | |
| − | + | * Get these data for EMSegmenter demonstrations: [[Media:EMSegmentTutorial.zip|EMSegmentTutorial.zip]] | |
| − | + | * Get these Tensor data for DTI Nrrd File Format demonstrations: [[Media:Tensor_data.zip| TensorData.zip]] | |
| − | + | * Get these Tensor data for DWI Nrrd File Format demonstrations: [[Media:Dwi-dicom.zip|dwi-dicom.zip]] | |
| − | + | * Get these data for fMRI demonstrations: [[Media:FMRIData1_short.zip|fMRIData_short.zip]], [[Media:FMRIData2_long.zip|fMRIData_long.zip]] | |
= Slicer Training = | = Slicer Training = | ||
| − | + | * Slicer Training 1: [[Media:SlicerTraining1LoadingAndViewingData.ppt|Loading and Viewing Data ]] '''''' | |
| − | + | * Slicer Training 2: [[Media:Slicer_Segmentation_Tutorial.ppt|Manual Segmentation and Model Making ]] | |
| − | + | * Slicer Training 3: [[Media:03-LevelSet.ppt|Level-Set Segmentation]] | |
| − | + | * Slicer Training 4: [[Media:Slicer_DTMRI_Training4.ppt| DT-MRI module ]] | |
| − | + | * Slicer Training 5: [[Media:SlicerTraining5_fMRI.ppt| fMRI module ]] | |
| − | + | * Slicer Training 6: [[Media:SlicerTraining6_vtkFreeSurferReaders.ppt| vtkFreeSurferReaders Module ]] | |
| − | + | * Slicer Training 7: [[Media:SlicerTraining7SavingData.ppt| Saving Data ]] | |
| − | + | * Slicer Training 8: [[Media:SlicerTraining8-NrrdFileFormat.ppt|Nrrd File Format]] | |
| − | + | * Slicer Training 9: [[Media:SlicerTraining9_DTI-FromDicomToNrrd.ppt|Dicom to Nrrd Conversion]] | |
| + | * Slicer Advanced Training 10 :[[Media:SlicerAdvancedTraining_EMBrainAtlasClassifier_V1.0.ppt| EMBrainAtlasClassifier ]] | ||
| − | = Slicer | + | = Slicer Additional Resources = |
| − | + | * [[BrainAtlas|SPL PNL Brain Atlas]] | |
| − | + | * [[IGT-Tutorials|IGT Tutorial Materials]] | |
| − | + | * [[Media:Training_EMLocalSegment_v1.pdf | EMSegmenter]] for multi-channel data and white matter hyperintensities | |
| − | |||
| − | |||
| − | |||
| − | |||
| + | = Feedback and Bug reports = | ||
| + | For course related questions, please send an e-mail to Sonia Pujol, Ph.D. (spujol at bwh.harvard.edu). | ||
| + | * [[Slicer:Feedback|Feedback about Slicer]] | ||
* [http://www.na-mic.org/Bug/ Bug reports] | * [http://www.na-mic.org/Bug/ Bug reports] | ||
| − | |||
= Acknowledgements = | = 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]] | <br /> Back to [[Training:Main|Training:Main]] | ||
Revision as of 21:37, 10 January 2007
Home < Slicer:Workshops:User Training 101This is the introductory Slicer 2.6 training material.
Contents
Introduction
You can begin to learn how to
- load and view data
- segment data and create 3D models
- use the DTI and fMRI modules
For an overview, dowload this slideshow
Software Installation
Please install the following software applications and files from the NAMIC site before the course: the current version of the Slicer program appropriate to your platform, the tutorial guide for Slicer, the generic sample data set. This material is located in Slicer 2.6 Getting Started: Software & Sample Data .
Data to Download
- Get the tutorial data with Dicom tutorial_with_dicom.zip
- Get this extra set of interoperative data mrt-images.zip
- Get this data for testing registrations reg-sample.zip
- Get these data for DTI demonstrations: SlicerSampleDTI.zip dwi-dicom.zip
- Get these data for FreeSurfer demonstrations: FreeSurferSubjects.zip
- Get these data for EMAtlasBrainClassifier demonstrations: BrainAtlasClassifier.zip
- Get these data for EMSegmenter demonstrations: EMSegmentTutorial.zip
- Get these Tensor data for DTI Nrrd File Format demonstrations: TensorData.zip
- Get these Tensor data for DWI Nrrd File Format demonstrations: dwi-dicom.zip
- Get these data for fMRI demonstrations: fMRIData_short.zip, fMRIData_long.zip
Slicer Training
- Slicer Training 1: Loading and Viewing Data '
- Slicer Training 2: Manual Segmentation and Model Making
- Slicer Training 3: Level-Set Segmentation
- Slicer Training 4: DT-MRI module
- Slicer Training 5: fMRI module
- Slicer Training 6: vtkFreeSurferReaders Module
- Slicer Training 7: Saving Data
- Slicer Training 8: Nrrd File Format
- Slicer Training 9: Dicom to Nrrd Conversion
- Slicer Advanced Training 10 : EMBrainAtlasClassifier
Slicer Additional Resources
- SPL PNL Brain Atlas
- IGT Tutorial Materials
- EMSegmenter for multi-channel data and white matter hyperintensities
Feedback and Bug reports
For course related questions, please send an e-mail to Sonia Pujol, Ph.D. (spujol at bwh.harvard.edu).
Acknowledgements
- Slicer is being developed by a community of contributors. For more information see the Slicer website.
Back to Training:Main
