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

From NAMIC Wiki
Jump to: navigation, search
m (Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/")
 
Line 16: Line 16:
 
The current version of Slicer that is fully supported is Slicer 2.6.  
 
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.  
+
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.  
  
  
Line 110: Line 110:
 
* [[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]
−
* [http://www.slicer.org/slicerWiki/index.php/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.
  

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

Retrieved from "https://www.na-mic.org/w/index.php?title=Slicer:Workshops:User_Training_101_SPujol&oldid=97698"