Difference between revisions of "EMSegmenter-Tasks"

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==What is a task?==
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[[EMSegmenter-Overview|Return to EMSegmenter Overview Page]]
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=What is a task?=
  
 
Most clinicians are using the EMSegmenter to segment specific parts of the human body. Those segmentations depend heavily on
 
Most clinicians are using the EMSegmenter to segment specific parts of the human body. Those segmentations depend heavily on
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The .tcl script is used to perform some pre-processing on the input data.<br>
 
The .tcl script is used to perform some pre-processing on the input data.<br>
 
<br>
 
<br>
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Visit the following web page to create your own [[EMSegmenter-CreateTask| task]] or we can [[ EMSegmenter-UseCaseAdvertisement | help ]] you .
  
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==Segmentation Task Library==
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=Segmentation Task Library=
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=Existing Tasks=
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==Existing Tasks in Slicer 3.6.3==
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There are currently 2 tasks defined in Slicer 3.6.2
 
 
*[[Image:MRI-Human-Brain_BeforeAfter.png|250px]] '''Task 01: [[EMSegmenter-Tasks:MRI-Human-Brain|MRI Human Brain ''' for non-skull stripped T1 scans]]
 
*[[Image:MRI-Human-Brain_BeforeAfter.png|250px]] '''Task 01: [[EMSegmenter-Tasks:MRI-Human-Brain|MRI Human Brain ''' for non-skull stripped T1 scans]]
 
*[[Image:MRIHumanBrainParcellation.png|250px]]  '''Task 02: [[EMSegmenter-Tasks:MRI-Human-Brain-Parcellation|MRI Human Brain Parcellation ''' for skull stripped T1 scans]]
 
*[[Image:MRIHumanBrainParcellation.png|250px]]  '''Task 02: [[EMSegmenter-Tasks:MRI-Human-Brain-Parcellation|MRI Human Brain Parcellation ''' for skull stripped T1 scans]]
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*[[Image:NHP.png|250px]] '''Task 03: [[EMSegmenter-Tasks:Non-Human-Primate|Non-Human Primate ''' for skull stripped T1 scans]]
  
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=Tasks in development=
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==Tasks for Slicer 3.6.4==
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*[[Image:NHP.png|250px]] '''Task 03: [[EMSegmenter-Tasks:Non-Human-Primate|Non-Human Primate ''' for skull stripped T1 scans]]
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* [[Image:EMS Result Hand subject2.png|250px]] '''Task 04: [[EMSegmenter-Tasks:CT-Hand-Bone|CT Hand Bone ''']]
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* CT Hand Bone
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* [[Image:MRIHumanBrainFullParcellation_before_after.png|250px]] '''Task 05: [[EMSegmenter-Tasks:MRI-Human-Brain-Full-Parcellation|MRI Human Brain Full Parcellation''' for non-skull stripped T1 scans]]
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* [[Image:MRIHumanBrainHIPR beforeafter.png|250px]] '''Task 06: [[EMSegmenter-Tasks:MRI-Human-Brain-HIPR|MRI Human Brain with high in-plane resolution''' for non-skull stripped T1 scans]]
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* [[Image:EMS_Hemisphere_before_after.png|250px]]'''Task 07: [[EMSegmenter-Tasks:MRI-Human-Brain-Hemisphere|MRI Human Brain Hemisphere''' for non-skull stripped T1 scans]]
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==Tasks in development==
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* [[Image:EMS HumanEye Before After.png|250px]]'''Task 08: [[EMSegmenter-Tasks:Human-Eye|Human Eye''']]
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* [[Image:EMS MRIHumanBrainExp Before After.png|250px]] '''Task 09: [[EMSegmenter-Tasks:MRI-Human-Brain-Experimental|MRI Human Brain Experimental''' with skull stripping]]
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* [[Image:EMSegment-CardioA1-grey-small.jpg|125px]][[Image:EMSegment CardioA1small.jpg|125px]] '''Task 10: [[EMSegmenter-Tasks:cineMARI|cine MRI''' ]]
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* [[Image:EMS LesionsExp BeforeAfter.png|250px]] '''Task 11: [[EMSegmenter-Tasks:LesionExp|White matter lesion segmentation''' ]]
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* '''Task 12: [[EMSegmenter-Tasks:EMS_Spine|Bone segmentation''' ]]
  
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==External Command Lines (Under Development) ==
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* [[Image:GLISTR Flair.png|125px]][[Image:GLISTR Seg.png|125px]]'''Task 12: [https://www.rad.upenn.edu/sbia/projects/glistr.html GLISTR: Automatic Glioma Segmentation'''] <BR> The software was developed and is distributed by SBIA. SBIA will soon release an interface for GLISTR to interact with Slicer
  
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=Task creation process - for developer=
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=Additional Use Cases=
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The goal is to create a task with the name 'Hello World'
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==Quantitative assessment using MPRAGE and Flair images==
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* Collaborator: Tammie Benzinger , Washington University School of Medicine
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* Short description: Quantitative assessment using MPRAGE and Flair images
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* Image specification: Dimension: 256x256x160 , Spacing 1x1x1, T2 MPRAGE
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* Used Task: [[EMSegmenter-Tasks:MRI-Human-Brain-Experimental|'''MRI Human Brain Experimental''' (with skull stripping)]]
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<gallery perrow=2: widths=200px : heights=200px>
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Image:EMS_Quantitative_assessment_orig.png
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Image:EMS_Quantitative_assessment.png
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</gallery>
  
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After following the instructions below the new task will consist of following files:
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==Brain Atrophy in Aging Patients==
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./Slicer3/Modules/EMSegment/Tasks/Hello-World.mrml
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* Collaborator: David Tate, PI (Brigham and Women's Hospital), Daniel McCaffrey (Brigham and Women's Hospital), Alex Zaitsev (Brigham and Women's Hospital/Surgical Planning Laboratory) and Jewish Hospital
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./Slicer3/Modules/EMSegment/Tasks/Hello-World.tcl
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* Short description: Evaluate Brain Atrophy in aging subjects (NOTE: the segmentation was done for old scans from 90s. No other tools could segment CSF.)
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./Slicer3/Modules/EMSegment/Tasks/Hello-World/<atlas_file_1>
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* Image specification: NA Tesla, Scanner: NA, Psuedo T1, Axial Scans, TR/TI/TE=NA, pixel_xsize = 0.937500, pixel_ysize = 0.937500, fov = 240.000000, aspect = 0.000000, thick = 5.000000
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./Slicer3/Modules/EMSegment/Tasks/Hello-World/<atlas_file_2>
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* Used Task: [[EMSegmenter-Tasks:MRI-Human-Brain|'''MRI Human Brain''']]
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[...]
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<gallery perrow=2: widths=200px : heights=200px>
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./Slicer3/Modules/EMSegment/Tasks/Hello-World/<atlas_file_i>
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Image:EMS_AgingStudy_DTate_Project_3-6-2.png
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[...]
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Image:EMS_AgingStudy_PseudoT1_OldMIRs_JewishHospEMS_manualTrain_60x.png
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./Slicer3/Modules/EMSegment/Tasks/Hello-World/<atlas_file_N>
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</gallery>
  
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==Brain Atrophy in HIV Patients==
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* Collaborator: David Tate, PI (Brigham and Women's Hospital), Troy Russel (Brigham and Women's Hospital), Alex Zaitsev (Brigham and Women's Hospital/Surgical Planning Laboratory) and National HIV Consortium
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* Short description: Evaluate Brain Atrophy in HIV Patients
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* Image specification: 3 Tesla, Scanner: NA, MPRAGE, Sagittal Scans, TR/TI/TE=NA, pixel_xsize = 0.9375, pixel_ysize = 0.9375, fov =  NA, aspect =  NA, space =  1.5
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* Used Task: [[EMSegmenter-Tasks:MRI-Human-Brain|'''MRI Human Brain''']]
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<gallery perrow=2: widths=425px : heights=200px>
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Image:EMS_HIVStudy_Segmentation.png
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Image:EMS_HIVStudy_Segmentation_Auto.png
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</gallery>
  
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* Create a new directory ./Slicer3/Modules/EMSegment/Tasks/Hello-World
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==Pediatric MS Study==
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* Collaborator: Tanuja Chitnis PI (Brigham and Women's Hospital/Multiple Sclerosis Center), Alexander Zaitsev (Brigham and Women's Hospital/Surgical Planning Laboratory) and Massachusetts General Hospital
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* Short description: Evaluate brain atrophy for pediatric MS Patients
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* Image specification: 3 Tesla, Scanner: SIGNA HDx / GE MEDICAL SYSTEMS, 3D MPRAGE, Sagital Scans, TR/TI/TE=24/0/7 ms, pixel_xsize = 0.976600, pixel_ysize = 0.976600, fov =  250.009598, aspect =  1.535941, thick =  1.500000, space =  0.000000
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* Used Task: [[EMSegmenter-Tasks:MRI-Human-Brain|'''MRI Human Brain''']]
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<gallery perrow=1: widths=630px : heights=210px>
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Image:EMS_PED_MS_Study_Segmentation.png
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</gallery>
  
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* Copy the atlas files for air, GM, T1 into this directory.
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==Social Cognition Study==
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* Collaborator: Collaborator: Andrea Mike, MD (Pecs University, Hungary), Charles Guttmann, MD, Alexander Zaitsev (Brigham and Women's Hospital)
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* Short description: Evaluate brain atrophy for elderly MS patients.
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* Number of processed cases: 50
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* Image specification: 3 Tesla, Scanner: Magnetom TIM Trio, Siemens, 3D MPRAGE, Slice thickness: 1.2mm, Spacing 1.2 1 1 (mm)
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* Used Task: [[EMSegmenter-Tasks:MRI-Human-Brain|'''MRI Human Brain''']]
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<gallery perrow=1: widths=630px : heights=200px>
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Image:EMS_SocialCognitionLESIONS_MANUALLY_SEGMENTED_PECS_S006_Seg.png
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</gallery>
  
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* Start Slicer
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==Physiological Brain Activity Longitudinal Study==
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* Switch to the EMSegmenter module
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* Collaborator: Laura Horky PI (Brigham and Women's Hospital(BWH)), Jon Hainer (BWH), Wendy Plesniak (BWH), Alexander Zaitsev (BWH), Ron Kikinis (BWH) and BWH Division of Nuclear Medicine
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* Create new task
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* Short description: Evaluate glycolitical brain activity in CSF and White Matter for the patients undergoing chemical therapy courses.
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**  Name:           Hello World
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* Image specification: 1.5 Tesla ,Scanner: SIGNA EXCITE / GE MEDICAL SYSTEMS, T1, Axial Scans, TR/TI/TE=500/0/21 ms, pixel_xsize = 0.781251, pixel_ysize = 0.781244, fov = 0.000000, aspect =  7.679990, thick =  5.000000, space =  1.000000
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**  Pre-processing: None
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* Used Task: [[EMSegmenter-Tasks:MRI-Human-Brain-Hemisphere|'''MRI Human Brain Hemisphere''']]
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* Basically follow our EMSegmenter advanced tutorial, but create a simple tree
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<gallery perrow=3: widths=250px  : heights=200px>
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** load ./Slicer3/Modules/EMSegment/Testing/TestData/MiscVolumeData/MRIHumanBrain_T1_aligned.nrrd
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Image:EmSegment PETCT 1.png
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** Add a channel, call it T1, assign MRIHumanBrain_T1_aligned
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Image:EmSegment PETCT 2.png
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**  Create a simple anatomical tree (air and GM)
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Image:EmSegment PETCT 3.png | Result on test data
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**  Load atlas files only from ./Slicer3/Modules/EMSegment/Tasks/Hello-World/
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</gallery>
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**  generate mean and covariance values
 
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**  specify node weights
 
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* At step 9/9. click on 'Create Template File'
 
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**  Save the file under ./Slicer3/Modules/EMSegment/Tasks/Hello-World.mrml
 
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** The target node and some other unneeded nodes will be removed from the mrml scene and written to disk.
 
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* Close Slicer
 
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* Copy our standard tcl file ./Slicer3/Modules/EMSegment/Tasks/Template.tcl to ./Slicer3/Modules/EMSegment/Tasks/Hello-World.tcl
 
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* Adjust this tcl file to include your pre-processing pipeline.
 
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* edit ./Slicer3/Modules/EMSegment/Tasks/Hello-World.tcl to specify your own pre-processing
 
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* edit ./Slicer3/Modules/EMSegment/Tasks/Hello-World.mrml to use your own pre-processing
 
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** - <EMS TclTaskFilename="GenericTask.tcl" ></EMS>
 
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** + <EMS TclTaskFilename="Hello-World.tcl" ></EMS>
 
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* touch ../Slicer3/Modules/EMSegment/CMakeLists.txt and do a 'make' to copy the new files into the binary directory
 
  
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<gallery perrow=3: widths=250px  : heights=200px>
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Image:EMSegment PETCT Physiology-1.png
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Image:EMSegment PETCT Physiology-2.png
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Image:EMSegment PETCT Physiology-3.png | Result on patient data
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</gallery>
  
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The result of the process above can also be downloaded here:
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==Comprehensive Longitudinal Investigation of Multiple Sclerosis at Brigham and Women’s Hospital (CLIMB) Study==
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After Installing both files this 'Hello World' task will appear in the task list under the name 'Hello World'.
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* [http://www.partnersmscenter.org/index.php?id=217&mn=9 CLIMB Study Web Page]
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* Collaborator: Svetlana Egorova MD/PhD (Brigham and Women's Hospital(BWH)), Alexander Zaitsev PhD (BWH)
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* Short description: Provide Basic EM Segmentation for estimation of brain parenchymal fraction (BPF) . The processing is being performed for the cases with failing PD TDS+ segmentation. The T1-type scans are segmented and registered to PD/T2 images. The requests are being submitted over the Web GUI.
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* Image specification: 1.5 Tesla ,Scanner: Varies among participants.
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* Used Task: [[EMSegmenter-Tasks:MRI-Human-Brain-Hemisphere|'''MRI Human Brain Hemisphere''']]

Latest revision as of 00:42, 6 August 2011

Home < EMSegmenter-Tasks

Return to EMSegmenter Overview Page


What is a task?

Most clinicians are using the EMSegmenter to segment specific parts of the human body. Those segmentations depend heavily on the used input data. The signal level in the input data varies with the used image modalities (e.g. MRI, CT, ...) and with each anatomical structure. The EMSegmenter can take advantage of some knowledge about the signal level of those anatomical structures in the different image modalities.
Technically, each tasks consist of a .mrml file and a .tcl file.
The .mrml file stores the anatomical properties (mean values, covariance values) in a user defined tree structure.
The .tcl script is used to perform some pre-processing on the input data.

Visit the following web page to create your own task or we can help you .

Segmentation Task Library

Existing Tasks in Slicer 3.6.3

Tasks for Slicer 3.6.4

Tasks in development

External Command Lines (Under Development)

Additional Use Cases

Quantitative assessment using MPRAGE and Flair images

  • Collaborator: Tammie Benzinger , Washington University School of Medicine
  • Short description: Quantitative assessment using MPRAGE and Flair images
  • Image specification: Dimension: 256x256x160 , Spacing 1x1x1, T2 MPRAGE
  • Used Task: MRI Human Brain Experimental (with skull stripping)
  • EMS Quantitative assessment orig.png
  • EMS Quantitative assessment.png

Brain Atrophy in Aging Patients

  • Collaborator: David Tate, PI (Brigham and Women's Hospital), Daniel McCaffrey (Brigham and Women's Hospital), Alex Zaitsev (Brigham and Women's Hospital/Surgical Planning Laboratory) and Jewish Hospital
  • Short description: Evaluate Brain Atrophy in aging subjects (NOTE: the segmentation was done for old scans from 90s. No other tools could segment CSF.)
  • Image specification: NA Tesla, Scanner: NA, Psuedo T1, Axial Scans, TR/TI/TE=NA, pixel_xsize = 0.937500, pixel_ysize = 0.937500, fov = 240.000000, aspect = 0.000000, thick = 5.000000
  • Used Task: MRI Human Brain
  • EMS AgingStudy DTate Project 3-6-2.png
  • EMS AgingStudy PseudoT1 OldMIRs JewishHospEMS manualTrain 60x.png

Brain Atrophy in HIV Patients

  • Collaborator: David Tate, PI (Brigham and Women's Hospital), Troy Russel (Brigham and Women's Hospital), Alex Zaitsev (Brigham and Women's Hospital/Surgical Planning Laboratory) and National HIV Consortium
  • Short description: Evaluate Brain Atrophy in HIV Patients
  • Image specification: 3 Tesla, Scanner: NA, MPRAGE, Sagittal Scans, TR/TI/TE=NA, pixel_xsize = 0.9375, pixel_ysize = 0.9375, fov = NA, aspect = NA, space = 1.5
  • Used Task: MRI Human Brain
  • EMS HIVStudy Segmentation.png
  • EMS HIVStudy Segmentation Auto.png

Pediatric MS Study

  • Collaborator: Tanuja Chitnis PI (Brigham and Women's Hospital/Multiple Sclerosis Center), Alexander Zaitsev (Brigham and Women's Hospital/Surgical Planning Laboratory) and Massachusetts General Hospital
  • Short description: Evaluate brain atrophy for pediatric MS Patients
  • Image specification: 3 Tesla, Scanner: SIGNA HDx / GE MEDICAL SYSTEMS, 3D MPRAGE, Sagital Scans, TR/TI/TE=24/0/7 ms, pixel_xsize = 0.976600, pixel_ysize = 0.976600, fov = 250.009598, aspect = 1.535941, thick = 1.500000, space = 0.000000
  • Used Task: MRI Human Brain
  • EMS PED MS Study Segmentation.png

Social Cognition Study

  • Collaborator: Collaborator: Andrea Mike, MD (Pecs University, Hungary), Charles Guttmann, MD, Alexander Zaitsev (Brigham and Women's Hospital)
  • Short description: Evaluate brain atrophy for elderly MS patients.
  • Number of processed cases: 50
  • Image specification: 3 Tesla, Scanner: Magnetom TIM Trio, Siemens, 3D MPRAGE, Slice thickness: 1.2mm, Spacing 1.2 1 1 (mm)
  • Used Task: MRI Human Brain
  • EMS SocialCognitionLESIONS MANUALLY SEGMENTED PECS S006 Seg.png

Physiological Brain Activity Longitudinal Study

  • Collaborator: Laura Horky PI (Brigham and Women's Hospital(BWH)), Jon Hainer (BWH), Wendy Plesniak (BWH), Alexander Zaitsev (BWH), Ron Kikinis (BWH) and BWH Division of Nuclear Medicine
  • Short description: Evaluate glycolitical brain activity in CSF and White Matter for the patients undergoing chemical therapy courses.
  • Image specification: 1.5 Tesla ,Scanner: SIGNA EXCITE / GE MEDICAL SYSTEMS, T1, Axial Scans, TR/TI/TE=500/0/21 ms, pixel_xsize = 0.781251, pixel_ysize = 0.781244, fov = 0.000000, aspect = 7.679990, thick = 5.000000, space = 1.000000
  • Used Task: MRI Human Brain Hemisphere
  • EmSegment PETCT 1.png
  • EmSegment PETCT 2.png

  • Result on test data

  • EMSegment PETCT Physiology-1.png
  • EMSegment PETCT Physiology-2.png

  • Result on patient data

Comprehensive Longitudinal Investigation of Multiple Sclerosis at Brigham and Women’s Hospital (CLIMB) Study

  • CLIMB Study Web Page
  • Collaborator: Svetlana Egorova MD/PhD (Brigham and Women's Hospital(BWH)), Alexander Zaitsev PhD (BWH)
  • Short description: Provide Basic EM Segmentation for estimation of brain parenchymal fraction (BPF) . The processing is being performed for the cases with failing PD TDS+ segmentation. The T1-type scans are segmented and registered to PD/T2 images. The requests are being submitted over the Web GUI.
  • Image specification: 1.5 Tesla ,Scanner: Varies among participants.
  • Used Task: MRI Human Brain Hemisphere
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