Latest revision as of 00:42, 6 August 2011

Home < EMSegmenter-Tasks

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

Task 01: MRI Human Brain for non-skull stripped T1 scans
Task 02: MRI Human Brain Parcellation for skull stripped T1 scans
Task 03: Non-Human Primate for skull stripped T1 scans

Tasks for Slicer 3.6.4

Task 04: CT Hand Bone
Task 05: MRI Human Brain Full Parcellation for non-skull stripped T1 scans
Task 06: MRI Human Brain with high in-plane resolution for non-skull stripped T1 scans
Task 07: MRI Human Brain Hemisphere for non-skull stripped T1 scans

Tasks in development

Task 08: Human Eye
Task 09: MRI Human Brain Experimental with skull stripping
Task 10: cine MRI
Task 11: White matter lesion segmentation
Task 12: Bone segmentation

External Command Lines (Under Development)

Task 12: GLISTR: Automatic Glioma Segmentation
The software was developed and is distributed by SBIA. SBIA will soon release an interface for GLISTR to interact with Slicer

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)

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

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

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

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

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

Result on test data

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

Difference between revisions of "EMSegmenter-Tasks"

Latest revision as of 00:42, 6 August 2011

Contents

What is a task?

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

Brain Atrophy in Aging Patients

Brain Atrophy in HIV Patients

Pediatric MS Study

Social Cognition Study

Physiological Brain Activity Longitudinal Study

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

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@@ Line 1: / Line 1: @@
-=Under construction=
+[[EMSegmenter-Overview|Return to EMSegmenter Overview Page]]
 =What is a task?=
@@ Line 12: / Line 13: @@
 The .tcl script is used to perform some pre-processing on the input data.<br>
 <br>
+Visit the following web page to create your own [[EMSegmenter-CreateTask| task]] or we can [[ EMSegmenter-UseCaseAdvertisement | help ]] you .
+=Segmentation Task Library=
+==Existing Tasks in Slicer 3.6.3==
+*[[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:NHP.png|250px]] '''Task 03: [[EMSegmenter-Tasks:Non-Human-Primate|Non-Human Primate ''' for skull stripped T1 scans]]
-=Existing Tasks=
+==Tasks for Slicer 3.6.4==
+* [[Image:EMS Result Hand subject2.png|250px]] '''Task 04: [[EMSegmenter-Tasks:CT-Hand-Bone|CT Hand Bone ''']]
-There are currently 2 tasks defined in Slicer 3.6.2
+* [[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]]
+* [[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]]
-==MRI Human Brain==
+* [[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]]
-===Description===
-MRI Human Head pipeline
-===Anatomical Tree===
-* ROOT
-** BG
-*** AIR
-*** Skull
-** ICC
-*** WM
-*** GM
-*** CSF
-===Result===
-[[Image:MRI-Human-Brain_BeforeAfter.png]]
-==MRI Human Brain Parcellation==
-===Description===
-MRI Human Head pipeline for a finer-grained parcellation
-===Anatomical Tree===
-Legend: <br>
-BG: background <br>
-LT: left temporal <br>
-GM: grey matter <br>
-WM: white matter <br>
-CSF: cerebrospinal fluid <br>
-<br>
-Tree:
-* Root
-** BG
-** GM
-*** LTGM
-**** LTGM1
-**** LTGM2
-**** LTGM3
-**** LTGM4
-*** RTGM
-**** RTGM1
-**** RTGM2
-**** RTGM3
-**** RTGM4
-*** SUBGM
-** WM
-*** LTWM
-**** LTWM1
-**** LTWM2
-**** LTWM3
-**** LTWM4
-*** RTWM
-**** RTWM1
-**** RTWM2
-**** RTWM3
-**** RTWM4
-*** SUBWM
-** CSF
-===Result===
-[[Image:MRIHumanBrainParcellation.png]]
-===Collaborators===
-Padmapriya Srinivasan and Sylvain Bouix (PNL-BWH)
-=Tasks in development=
-==Non-Human Primate==
-===Legend===
-BG: background <br>
-LT: left temporal <br>
-GM: grey matter <br>
-WM: white matter <br>
-CSF: cerebrospinal fluid <br>
-cau: caudate <br>
-put: putamen <br>
-hip: hippocampus <br>
-ICC: Intracranial Cavity <br>
-WGC: <br>
-lSGM: <br>
-rSGM: <br>
-BS: <br>
-CB: <br>
-<br>
-===Anatomical Tree===
-* Root
-** Head
-*** ICC
-**** WGC
-***** GM
-****** lSGM
-******* lcau
-******* lput
-******* lhip
-****** rSGM
-******* rcau
-******* rput
-******* rhip
-****** GMleaf
-***** WM
-***** CSF
-**** BS
-**** CB
-*** rest
-===Result===
+==Tasks in development==
-[[Image:NHP.png]]
+* [[Image:EMS HumanEye Before After.png|250px]]'''Task 08: [[EMSegmenter-Tasks:Human-Eye|Human Eye''']]
+* [[Image:EMS MRIHumanBrainExp Before After.png|250px]] '''Task 09: [[EMSegmenter-Tasks:MRI-Human-Brain-Experimental|MRI Human Brain Experimental''' with skull stripping]]
+* [[Image:EMSegment-CardioA1-grey-small.jpg|125px]][[Image:EMSegment CardioA1small.jpg|125px]] '''Task 10: [[EMSegmenter-Tasks:cineMARI|cine MRI''' ]]
+* [[Image:EMS LesionsExp BeforeAfter.png|250px]] '''Task 11: [[EMSegmenter-Tasks:LesionExp|White matter lesion segmentation''' ]]
+* '''Task 12: [[EMSegmenter-Tasks:EMS_Spine|Bone segmentation''' ]]
+==External Command Lines (Under Development) ==
+* [[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
-===Collaborators===
+=Additional Use Cases=
-Andriy Fedorov (BWH)
+==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: [[EMSegmenter-Tasks:MRI-Human-Brain-Experimental|'''MRI Human Brain Experimental''' (with skull stripping)]]
+<gallery perrow=2: widths=200px : heights=200px>
+Image:EMS_Quantitative_assessment_orig.png
+Image:EMS_Quantitative_assessment.png
+</gallery>
-==CT Hand Bone==
+==Brain Atrophy in Aging Patients==
-===Collaborators===
+* 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
-TBD
+* 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: [[EMSegmenter-Tasks:MRI-Human-Brain|'''MRI Human Brain''']]
+<gallery perrow=2: widths=200px : heights=200px>
+Image:EMS_AgingStudy_DTate_Project_3-6-2.png
+Image:EMS_AgingStudy_PseudoT1_OldMIRs_JewishHospEMS_manualTrain_60x.png
+</gallery>
-==Task creation process - for developer==
+==Brain Atrophy in HIV Patients==
-The goal is to create a task with the name 'Hello World'
+* 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: [[EMSegmenter-Tasks:MRI-Human-Brain|'''MRI Human Brain''']]
+<gallery perrow=2: widths=425px : heights=200px>
+Image:EMS_HIVStudy_Segmentation.png
+Image:EMS_HIVStudy_Segmentation_Auto.png
+</gallery>
-After following the instructions below the new task will consist of following files:
+==Pediatric MS Study==
- ./Slicer3/Modules/EMSegment/Tasks/Hello-World.mrml
+* 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
- ./Slicer3/Modules/EMSegment/Tasks/Hello-World.tcl
+* Short description: Evaluate brain atrophy for pediatric MS Patients
-  ./Slicer3/Modules/EMSegment/Tasks/Hello-World/<atlas_file_1>
+* 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
-  ./Slicer3/Modules/EMSegment/Tasks/Hello-World/<atlas_file_2>
+* Used Task: [[EMSegmenter-Tasks:MRI-Human-Brain|'''MRI Human Brain''']]
-  [...]
+<gallery perrow=1: widths=630px : heights=210px>
- ./Slicer3/Modules/EMSegment/Tasks/Hello-World/<atlas_file_i>
+Image:EMS_PED_MS_Study_Segmentation.png
- [...]
+</gallery>
- ./Slicer3/Modules/EMSegment/Tasks/Hello-World/<atlas_file_N>
+==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: [[EMSegmenter-Tasks:MRI-Human-Brain|'''MRI Human Brain''']]
+<gallery perrow=1: widths=630px : heights=200px>
+Image:EMS_SocialCognitionLESIONS_MANUALLY_SEGMENTED_PECS_S006_Seg.png
+</gallery>
-* Create a new directory ./Slicer3/Modules/EMSegment/Tasks/Hello-World
+==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: [[EMSegmenter-Tasks:MRI-Human-Brain-Hemisphere|'''MRI Human Brain Hemisphere''']]
+<gallery perrow=3: widths=250px  : heights=200px>
+Image:EmSegment PETCT 1.png
+Image:EmSegment PETCT 2.png
+Image:EmSegment PETCT 3.png | Result on test data
+</gallery>
-* Copy the atlas files for air, GM, T1 into this directory.
+<gallery perrow=3: widths=250px  : heights=200px>
+Image:EMSegment PETCT Physiology-1.png
+Image:EMSegment PETCT Physiology-2.png
+Image:EMSegment PETCT Physiology-3.png | Result on patient data
+</gallery>
-* Start Slicer
+==Comprehensive Longitudinal Investigation of Multiple Sclerosis at Brigham and Women’s Hospital (CLIMB) Study==
-* Switch to the EMSegmenter module
+* [http://www.partnersmscenter.org/index.php?id=217&mn=9 CLIMB Study Web Page]
-* Create new task
+* Collaborator: Svetlana Egorova MD/PhD (Brigham and Women's Hospital(BWH)), Alexander Zaitsev PhD (BWH)
-**  Name:           Hello World
+* 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.
-**  Pre-processing: None
+* Image specification: 1.5 Tesla ,Scanner: Varies among participants.
-* Basically follow our EMSegmenter advanced tutorial, but create a simple tree
+* Used Task: [[EMSegmenter-Tasks:MRI-Human-Brain-Hemisphere|'''MRI Human Brain Hemisphere''']]
-** load ./Slicer3/Modules/EMSegment/Testing/TestData/MiscVolumeData/MRIHumanBrain_T1_aligned.nrrd
-** Add a channel, call it T1, assign MRIHumanBrain_T1_aligned
-**  Create a simple anatomical tree (air and GM)
-**  Load atlas files only from ./Slicer3/Modules/EMSegment/Tasks/Hello-World/
-**  generate mean and covariance values
-**  specify node weights
-* At step 9/9. click on 'Create Template File'
-**  Save the file under ./Slicer3/Modules/EMSegment/Tasks/Hello-World.mrml
-**  The target node and some other unneeded nodes will be removed from the mrml scene and written to disk.
-* Close Slicer
-* Copy our standard tcl file ./Slicer3/Modules/EMSegment/Tasks/Template.tcl to ./Slicer3/Modules/EMSegment/Tasks/Hello-World.tcl
-* Adjust this tcl file to include your pre-processing pipeline.
-* edit ./Slicer3/Modules/EMSegment/Tasks/Hello-World.tcl to specify your own pre-processing
-* edit ./Slicer3/Modules/EMSegment/Tasks/Hello-World.mrml to use your own pre-processing
-** - <EMS TclTaskFilename="GenericTask.tcl" ></EMS>
-** + <EMS TclTaskFilename="Hello-World.tcl" ></EMS>
-* touch ../Slicer3/Modules/EMSegment/CMakeLists.txt and do a 'make' to copy the new files into the binary directory