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[[Image:Nac.png|thumb|right|[http://nac.spl.harvard.edu 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 [http://www.slicer.org/slicerWiki/index.php/Slicer3.6:Training#Software_tutorials 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 [[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 [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.

= 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" cellpadding="5"
|- 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| Dicom to Nrrd 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]]
* [[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]
* [http://www.slicer.org/slicerWiki/index.php/SlicerOnBIRN How to use Slicer with BIRN]
* 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
* [http://www.airwayinspector.org/ Airway inspector]: 3D Slicer based tool for morphometry analysis of the lung airways and emphysema.

= Feedback  =

* [http://www.slicer.org/pages/Slicer_Community 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]]

[[Category:Slicer]]