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

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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>
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<div class="thumb tright"><div style="width: 90px">[[Image:Nac.png|[[Image:Nac.png|Link to the NAC website]]]]<div  
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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 neuroimage analysis using Slicer2.6.
+
This is a training compendium for neuroimage analysis using 3DSlicer.
−
You can begin to learn how to
+
 
 +
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
 
* perform Diffusion Tensor Imaging and fMRI analysis
 
* 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]]
 +
 
 +
= 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 [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.
 +
 
 +
 
 +
 
  
 
= Training Compendium =
 
= Training Compendium =
 +
 
For course related questions, please send an e-mail to Sonia Pujol, Ph.D. (spujol at bwh.harvard.edu).
 
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).]]
 
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* Training 1: [[Media:SlicerTraining1LoadingAndViewingData.ppt| Loading and Viewing Data ]] 
 
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* Training 2: [[Media:Slicer_Segmentation_Tutorial.ppt|Manual Segmentation and Model Making ]] 
 
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* Training 3: [[Media:03-LevelSet.ppt|Level-Set Segmentation ]]
 
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* Training 4: [[Media:Slicer_DTMRI_Training4.ppt|Diffusion Tensor Imaging Analysis  ]]
 
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* Training 5: [[Media:SlicerTraining5_fMRI.ppt| Functional Magnetic Resonance Imaging Analysis ]]
 
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* Training 6: [[Media:SlicerTraining6_vtkFreeSurferReaders.ppt| FreeSurferReader ]]
 
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* Training 7: [[Media:SlicerTraining7SavingData.ppt|Volume, Model and Scene Saving ]]
 
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* Training 8: [[Media:SlicerTraining8-NrrdFileFormat.ppt|Nrrd File Format]]
 
−
* Training 9: [[Media:SlicerTraining9_DTI-FromDicomToNrrd.ppt|Dicom to Nrrd Conversion]]
 
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* Advanced Training 10: [[Media:SlicerAdvancedTraining_EMBrainAtlasClassifier_V1.0.ppt|Automatic Segmentation of Brain Structures ]]
 
−
* Advanced Training 11: [[Media:SlicerAdvancedTraining11_Registration.ppt|Registration ]]
 
  
−
= Training Datasets =
+
[[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).]]
−
* 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]]
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{| border="2"
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* Get these data for Training 5: [[Media:FMRIData1_short.zip|fMRIData_short.zip]], [[Media:FMRIData2_long.zip|fMRIData_long.zip]]
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|- bgcolor="white"
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* Get these data for Training 6: [[Media:FreeSurferSubjects.zip|FreeSurferSubjects.zip ]]
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| ''''''
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* Get these data for Training 7: [[Media:Tutorial-with-dicom.zip|tutorial_with_dicom.zip]]
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| '''Course'''
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* Get these data for Training 8: [[Media:Tensor_data.zip| TensorData.zip]]
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| '''Dataset'''
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* Get these data for Training 9: [[Media:Dwi-dicom.zip|dwi-dicom.zip]]
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|- bgcolor="white"
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* Get these data for Training 10: [[Media:BrainAtlasClassifier.zip|BrainAtlasClassifier.zip]]
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||[[Image:Training1 LoadingViewing.PNG|50px]]
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* Get these data for Training 11: [[Media:RegistrationSample.zip|RegistrationSample.zip]]
+
|
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* Get these extra set of interoperative data [[Media:Mrt-images.zip| mrt-images.zip]]
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[[Media:SlicerTraining1LoadingAndViewingData.ppt| Data Loading and Visualization ]]
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* Get these data for EMSegmenter demonstrations: [[Media:EMSegmentTutorial.zip|EMSegmentTutorial.zip]]
+
|
 +
[[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]]
 +
|
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[[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 ]]
 +
|}
  
−
= 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 =
 
= Slicer Additional Resources =
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* [[BrainAtlas|SPL PNL Brain Atlas]]
 
* [[BrainAtlas|SPL PNL Brain Atlas]]
 
* [[IGT-Tutorials|IGT Tutorial Materials]]
 
* [[IGT-Tutorials|IGT Tutorial Materials]]
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* [[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]]
 
* [[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]
−
* [[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.
 
* [[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]]
+
* [http://www.slicer.org/pages/Slicer_Community Feedback about Slicer]
 
* [http://www.na-mic.org/Bug/ Bug reports]
 
* [http://www.na-mic.org/Bug/ Bug reports]
  

Latest revision as of 18:07, 10 July 2017

Home < Slicer:Workshops:User Training 101 SPujol

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 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

Nrrd to Dicom 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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