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| ==Tutorials== | | ==Tutorials== |
| '''Tutorials for Biomedical Engineers and Clinical Research Users of the NA-MIC Kit''' | | '''Tutorials for Biomedical Engineers and Clinical Research Users of the NA-MIC Kit''' |
− | * [[Media:Stochastic_June09_1.ppt|Python Stochastic Tractography Module]]
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− | * [[media:Slicer3Training_WhiteMatterLesions_v2.3.pdf|White Matter Lesion Classification]]
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− | * [[media:DBP2JohnsHopkinsTransRectalProstateBiopsy_TutorialPres2009June.pdf|Trans-rectal MR guided prostate biopsy]] and [[Media:PerkStationSlicerTutorial.pdf|PerkStationSlicerTutorial]]
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− | * [[media:ARCTIC-Slicer3-Tutorial.ppt|ARCTIC: Automatic Regional Cortical ThICkness]]
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− | * [[media:Microscopy-Confocal-TrainingTutorial-2009JUNE.pdf|Confocal Microscopy]]
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− | * [[media:EMSegment_TrainingTutorial.pdf| Non-human Primates Segmentation Tutorial]]
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− | * [[AHM 2010 Tutorial Contest - Hammer Registration | Hammer Registration for Brain MRI]]
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− | * [[AHM 2010 Tutorial Contest - CoronaryArteriesCenterlinesVMTK | Centerline Extraction of Coronary Arteries using VMTK]]
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− | * [[AHM 2010 Tutorial Contest - EM Fiber Clustering| EM Fiber Clustering]]
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| + | | style="width:0%" | |
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| + | [[Media:Stochastic_June09_1.ppt|Python Stochastic Tractography Module]] |
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| + | [[media:Slicer3Training_WhiteMatterLesions_v2.3.pdf|White Matter Lesion Classification]] |
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| + | [[media:DBP2JohnsHopkinsTransRectalProstateBiopsy_TutorialPres2009June.pdf|Trans-rectal MR guided prostate biopsy]] and [[Media:PerkStationSlicerTutorial.pdf|PerkStationSlicerTutorial]] |
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| + | [[media:ARCTIC-Slicer3-Tutorial.ppt|ARCTIC: Automatic Regional Cortical ThICkness]] |
| + | |- |
| + | |
| + | | | |
| + | | | |
| + | [[media:Microscopy-Confocal-TrainingTutorial-2009JUNE.pdf|Confocal Microscopy]] |
| + | |- |
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| + | [[media:EMSegment_TrainingTutorial.pdf| Non-human Primates Segmentation Tutorial]] |
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| + | [[AHM 2010 Tutorial Contest - Hammer Registration | Hammer Registration for Brain MRI]] |
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| + | | | |
| + | | | |
| + | [[AHM 2010 Tutorial Contest - CoronaryArteriesCenterlinesVMTK | Centerline Extraction of Coronary Arteries using VMTK]] |
| + | |- |
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| + | | | |
| + | | | |
| + | [[AHM 2010 Tutorial Contest - EM Fiber Clustering| EM Fiber Clustering]] |
| + | |
| + | |} |
| '''Additional Tutorials''' | | '''Additional Tutorials''' |
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| *[http://www.slicer.org/slicerWiki/index.php/Slicer3.4:Training Slicer Training] | | *[http://www.slicer.org/slicerWiki/index.php/Slicer3.4:Training Slicer Training] |
The following is a collection of electronic resources provided by NA-MIC. This includes software, data, tutorials, presentations, and additional documentation.
Software
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Download Slicer
A general purpose biomedical computing application with extensive built-in visualization and analysis capabilities, accessible through an easy to use graphical interface.
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Download the NA-MIC Kit, including Slicer
The NA-MIC Kit is a free open source software platform. The NA-MIC Kit is distributed under a BSD-style license without restrictions or "give-back" requirements and is intended for research, but there are no restrictions on other uses. It consists of the 3D Slicer application software, a number of tools and toolkits such as VTK and ITK, and a software engineering methodology that enables multiplatform implementations.
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Data
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Brain: Multi-modality (sMRI, DTI, fMRI)
There are 20 cases: ten are Normal Controls and ten are Schizophrenic. Each case includes a weighted T1 scan, a weighted T2 scan, an fMRI scan, a DTI volume, the DWI with 51 directions, and several masks and labelmaps. Available from Harvard.
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Brain: 2-4 Year Old
Data for 2 autistic children and 2 normal controls (male, female) scanned at 2 years with follow up at 4 years from a 1.5T Siemens scanner. Files include structural data, tissue segmentation label map and subcortical structures segmentation. Available from UNC.
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Prostate: 5 cases
MRI Prostate data. 5 datasets, sagittal and axial scans, with and without needle. Available from Queens.
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Prostate: 10 cases
MRI Prostate data. 10 datasets, including a derived segmentation series with labelmaps. Available from Harvard.
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Prostate: Transrectal Tutorial Dataset
Transrectal Prostate Biopsy Tutorial Dataset. Walks the user through: Calibration (calibration image for the APT-MRI device), Segmentation (prostate MRI image and seeds for random walk segmentation algorithm), Targeting (target planning prostate MRI image), and Verification (needle insertion verification image). Available from Queens.
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Spine Phantom: PerkStation Tutorial Dataset
Perkstation Tutorial Dataset. Available from Queens.
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Visible Human Datasets
Visible Human Datasets with some post-processing. Available from Iowa.
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Registration Case Library Home Page
Many datasets available so that you can find a case similar enough to your particular image registration problem so that you can copy registration parameters, strategies, and tutorials. Successful registration strategies; algorithm choice and parameters vary greatly for different image contrast and content. Each listed case comprises a test dataset to try yourself, a guided step-by-step tutorial that will show you how to register the case with 3DSlicer, the solution transform so you can compare, and a custom Registration Parameter Presets file with optimized registration parameters that you can load directly into slicer.
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Tutorials
Tutorials for Biomedical Engineers and Clinical Research Users of the NA-MIC Kit
Additional Tutorials