Difference between revisions of "User:Pieper"

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== Summer 2009 Projects by Category ==
 +
 +
=== Applications/Analysis ===
 +
 +
#[[Measuring Alcohol Stress Interaction]] (Vidya Rajgopalan Virginia Tech)
 +
#[[2009_Summer_Project_Week_Lupus_Lesion_Segmentation |Lupus Lesion Segmentation]] (Jeremy Bockholt MRN)
 +
#[[2009_Summer_Project_Week_TrigeminalNerve|Atlas to CT Registration in Trigeminal Neuralgia]] (Marta Peroni PoliMI)
 +
#[[Summer2009:VCFS|Stochastic Tractography to study VCFS and Schizophrenia]] (Sylvain Bouix BWH)
 +
#[[2009_Summer_Project_Week_Meningioma_growth_simulation|Meningioma growth simulation]] (Andrey Fedorov BWH)
 +
#[[2009_Summer_Project_Week_Multimodal_SPL_Brain_Atlas|Linking atlas data with ontologies of brain morphology and function]] (Ion-Florin Talos BWH)
 +
#[[2009_Summer_Project_Week_MRSI-Module|MRSI Module]] (Bjoern Menze MIT)
 +
#[[2009_Summer_Project_Week_4D_Imaging| 4D Imaging (Perfusion, Cardiac, etc.) ]] (Junichi Tokuda BWH)
 +
#[[2009_Summer_Project_Week_4D_Gated_US_In_Slicer |Gated 4D ultrasound reconstruction for Slicer3]] (Danielle Pace Robarts Institute)
 +
#[[2009_Summer_Project_Week_Statistical_Toolbox |multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data]] (Diego Cantor Robarts Institute)
 +
 +
=== Segmentation ===
 +
 +
#[[2009_Summer_Project_Week_WML_SEgmentation |White Matter Lesion segmentation]] (Minjeong Kim UNC)
 +
#[[2009_Summer_Project_Week_Skull_Stripping | Skull Stripping]] (Snehasish Roy JHU)
 +
#[[EMSegment|EM Segment]] (Sylvain Jaume MIT, Nicolas Rannou BWH)
 +
#[[2009_Summer_Project_Week-FastMarching_for_brain_tumor_segmentation |FastMarching for brain tumor segmentation]] (Andrey Fedorov BWH)
 +
#[[2009_Summer_Project_Week_New_ITK_Level_Set_Framework|New Level Set Framework in ITK]] (Arnaud Gelas, Harvard Medical School)
 +
#[[2009_Summer_Project_Week_TubularSurfaceSeg|Tubular Surface Segmentation in Slicer]] (Vandana Mohan, Georgia Tech)
 +
# [[Summer2009:The Vascular Modeling Toolkit in 3D Slicer | The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn BWH)
 +
#[[2009_Summer_Project_Week_Slicer3_Cortical_Thickness_Pipeline|Cortical Thickness Pipeline]] (Clement Vachet UNC)
 +
#[[2009_Summer_Project_Week_Automatic_Brain_MRI_Pipeline|Automatic brain MRI processing pipeline]] (Marcel Prastawa Utah)
 +
#[[2009_Summer_Project_Week_Project_Segmentation_of_Muscoskeletal_Images|Segmentation of Knee Structures]] (Harish Doddi Stanford)
 +
#[[2009_Summer_Project_Week_Spherical_Mesh_Diffeomorphic_Demons_Registration |Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez Kitware)
 +
#[[2009_Summer_Project_Week_HAMMER_Registration | HAMMER Registration]] (Guorong Wu UNC)
 +
 +
=== Registration ===
 +
 +
# [[BSpline Registration in Slicer3 | BSpline Registration in Slicer3]] (Samuel Gerber Utah)
 +
# [[Summer2009:Registration reproducibility in Slicer|Registration reproducibility in Slicer3]] (Andrey Fedorov BWH)
 +
#[[2009_Summer_project_week_prostate_registration|Prostate Registration Slicer Module]] (Yi Gao, Georgia Tech)
 +
#[[2009_Summer_Project_Week_Slicer3_registration| Slicer 3 registration ]] (Andrew Rausch BWH PNL)
 +
# [[EPI Correction in Slicer3 | EPI Correction in Slicer3]] (Ran Tao Utah)
 +
#[[2009_Summer_Project_Week_Registration_for_RT|2d/3d Registration (and GPGPU acceleration) for Radiation Therapy]] (Tina Kapur BWH)
 +
 +
=== IGT ===
 +
 +
#[[2009_Summer_Project_Week_Transrectal_Prostate_biopsy|Transrectal Prostate Biopsy]] (Andras Lasso Queen's)
 +
#[[2009_Summer_Project_Week_Prostate_Robotics |Prostate Robotics]] (Junichi Tokuda BWH)
 +
#[[2009_Summer_Project_Week_Liver_Ablation_Slicer|Liver Ablation in Slicer]] (Ziv Yaniv Georgetown)
 +
#[[2009_Summer_Project_Week_Slicer3_Brainlab_Introduction|Demo of Neuronavigation using Brainlab, Slicer3, BioImage Suite]] (Haiying Liu BWH)
 +
#[[2009_Summer_Project_Week_3DGRASE|3D GRASE]] (Scott Hoge BWH)
 +
#[[2009_Summer_Project_Week_RTHawk_MR_Navigation|Using RTHawk to Implement MR Navigation]] (Ben Schwartz BWH)
 +
#[[2009_Summer_Project_Week_Slicer|Integration of Flexible Surgical Instrument Modeling and Virtual Catheter with Slicer]] (Jayender Jagadeesan BWH)
 +
# [[Integration of stereo video into Slicer3]] (Mehdi Esteghamatian Robarts Institute)
 +
 +
=== Radiotherapy ===
 +
 +
#[[2009_Summer_Project_Week_Slicer3_Adaptive_Radiotherapy|Adaptive Radiotherapy - Deformable registration and DICOMRT]] (Greg Sharp MGH)
 +
#[[2009_Summer_Project_Week_Adaptive_RT| Adaptive Radiotherapy for Head,Neck, and Thorax]] (Ivan Kolesov GATech)
 +
#[[2009_Summer_Project_Week_Cone_Beam_backprojection]](Zhou Shen U Michigan)
 +
#[[2009_Summer_project_week_3d_Deformable_alignment]](Dan McShan U Michigan)
 +
#[[2009_Summer_Project_Week_Dose_Calculation |accelerate calculation for LDR seeds]] (Jack Blevins Acousticmed)
 +
 +
=== Informatics ===
 +
 +
#[[2009_Summer_Project_Week_Slicer3_XNAT_UI | XNAT user interface improvements for NA-MIC]] (Dan Marcus WUSTL)
 +
#[[2009_Summer_Project_Week_XNATFS | XNAT File System with FUSE]] (Dan Marcus WUSTL)
 +
#[[2009_Summer_Project_Week_XNAT_i2b2|XNAT integration into Harvard Catalyst i2b2 framework]] (Yong Harvard)
 +
#[[2009_Summer_Project_Week_GWE_XNAT | GWE-XNAT Integration]] (Marco Ruiz UCSD)
 +
#[[2009_Summer_Project_Week_GWE_Results_Browser | GWE Results Browser Improvements]] (Marco Ruiz UCSD)
 +
 +
=== Diffusion ===
 +
 +
#[[2009_Summer_Project_Week_FunctionalClusteringAnalysis|Functional Analysis of White Matter in Whole Brain Clustering of Schizophrenic Patients]] (Doug Terry BWH)
 +
#[[2009_Summer_Project_Week_Slicer3_Fibre_Dispersion|Slicer module for the computation of fibre dispersion and curving measures]] (Peter Savadjiev BWH)
 +
#[[2009_Summer_Project_Week_DWI_/_DTI_QC_and_Prepare_Tool:_DTIPrep | DWI/DTI QC and Preparation Tool: DTIPrep]] (Zhexing Liu UNC)
 +
#[[2009_Summer_Project_Week_Hageman_DTIDigitalPhantom | DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA ]] (Nathan Hageman UCLA)
 +
#[[2009_Summer_Project_Week_Hageman_FMTractography | Fluid mechanics tractography and visualization]] (Nathan Hageman UCLA)
 +
 +
=== CUDA ===
 +
 +
#[[Summer2009:Using_CUDA_for_stochastic_tractography|Developing interactive stochastic tractography using CUDA]] (Julien de Siebenthal BWH)
 +
#acceleration of parallel real time processing of strain and elasticity images for monitoring of ablative therapy (Clif Burdette Acousticmed)
 +
 +
=== Python ===
 +
 +
# [[Summer2009:Using_ITK_in_python| Using ITK in python]] (Steve Pieper BWH)
 +
# [[Summer2009:Using_cython| Accelerating python with cython: application to stochastic tractography]] (Julien de Siebenthal BWH)
 +
# [[Summer2009:Implementing_parallelism_in_python| Taking advantage of multicore machines & clusters with python]] (Julien de Siebenthal BWH)
 +
# [[Summer2009:Using_client_server_paradigm_with_python_and_slicer| Deferring heavy computational tasks with Slicer python]] (Julien de Siebenthal BWH)
 +
 +
=== Slicer Internals ===
 +
 +
# [[2009_Summer_Project_Week_VTK_3D_Widgets_In_Slicer3|VTK 3d Widgets in Slicer3]] (Nicole Aucoin BWH)
 +
# [[2009_Summer_Project_Week_Colors_Module |Updates to Slicer3 Colors module]] (Nicole Aucoin BWH)
 +
#[[2009_Summer_Project_Week_Orthogonal_Reformat_Widget|Orthogonal Planes in Reformat Widget]] (Michal Depa MIT)
 +
# [[Slicer3 Informatics Workflow Design & XNAT updates | Slicer3 Informatics Workflow Design & XNAT updates for Slicer]] (Wendy Plesniak BWH)
 +
#[[2009_Summer_Project_Week_Extension_Manager|Slicer3 Extension Manager]] (Katie Hayes BWH)
 +
# [[MeshingSummer2009 | IAFE Mesh Modules - improvements and testing]] (Curt Lisle Knowledge Vis)
 +
 +
=== Execution Model ===
 +
 +
# [[Plug-In 3D Viewer based on XIP|Plug-in 3D Viewer based on XIP]] (Lining Yang Siemens Research)
 +
# [[Summer2009:Extension of the Command Line XML Syntax/Interface | Extension of the Command Line XML Syntax/Interface]] (Bennett Landman)

Revision as of 13:50, 22 June 2009

Steve Pieper of Isomics, Inc., is the Core PI for NAMIC Dissemination and Site PI for the BWH activities in the Engineering Core.

Email: pieper at bwh.harvard.edu

Information about my Ph.D. thesis research is at http://www.isomics.com/caps.

Handy Links

Pieper Home Page on slicer.org

Slicer3:EC2

http://pieper.wikispaces.com/

vim settings

Get to them on windows with 

:e $VIM/_vimrc

or on unix with 

:e ~/.vimrc

The values I use are: 


 " Steve Pieper's VIM preferences
 
 set nocompatible
 source $VIMRUNTIME/vimrc_example.vim
 source $VIMRUNTIME/mswin.vim
 "behave mswin
 "
 behave xterm
 
 set wildmode=longest,list
 
 set clipboard=unnamed
 
 set softtabstop=2
 set expandtab
 set tabstop=2
 set shiftwidth=2
 set autoindent
 set showmatch
 set laststatus=2

 set matchpairs+=<:> " To match arguments of templates
 set cinoptions={1s,:0,l1,g0,c0,(0,(s,m1 " ITK/VTK style indenting
 
 set vb
 syntax on
 
 " cycle through buffers with control page up/down
 map <C-PageDown> :bn
 map <C-PageUp> :bp
 " delete current buffer with control delete
 map <C-Del> :bd
 
 " cycle through tags with control right/left
 map <C-Right> :tn
 map <C-Left> :tp

cygwin

My windows c:/cygwin/cygwin.bat (launched by the shortcut). Requires rxvt and tcsh for cygwin. This is better for me because rxvt uses X-style cut and paste (middle mouse to paste) and tcsh can file complete with the drive letter (e.g. c:/Pro<Tab> --> c:/Program\ Files/ which bash won't do). 

@echo off

C:
chdir C:\cygwin\bin

set CYGWIN=binmode tty ntsec

rxvt -e /bin/tcsh -l

REM bash --login -i


tcsh aliases

Simple aliases for controlling the title bar of an xterm (or compatible terminal emulator) to keep track of where you are: 

alias xt 'echo -n "\033]0;\!*\007"'
alias cd 'xt \!*; chdir \!*'
alias ssh 'xt \!*; \ssh \!*; xt `hostname`'

Benchmarks

Slicer:benchmarks

Launching visual studio for slicer3 debugging

The you need to have the library paths set up correctly or the debugger won't find the dlls. In the Slicer3-build directory made by getbuildtest.tcl: 

./Slicer3.exe --launch c:/Program\ Files/Microsoft\ Visual\ Studio\ 8/Common7/IDE/devenv.exe --detach Slicer3.sln

or, for the free Visual Studio Express 2005: 

 ./Slicer3.exe --launch c:/Program\ Files/Microsoft\ Visual\ Studio\ 8/Common7/IDE/VCExpress.exe --detach Slicer3.sln

or, for the free Visual Studio Express 2008: 

 ./Slicer3.exe --launch c:/Program\ Files/Microsoft\ Visual\ Studio\ 9.0/Common7/IDE/VCExpress.exe --detach Slicer3.sln

For 64 bit windows 2005: 

./Slicer3.exe --launch "c:/Program Files (x86)/Microsoft Visual Studio 8/Common7/IDE/devenv.exe" --detach Slicer3.sln

Then go to the Slicer3-real project and right click on it and select Set As Startup Project from the menu. Then you can use F5 to compile and start the debugger.

Wiki backup

A quick and dirty way of backing up the wiki: 

wget -r http://wiki.na-mic.org

as of January 2007, this results in 3.3G. This doesn't preserve the full history or wiki markup, but it's an easy way to get piece of mind.

Format Test

A page testing format options.

Pages with nice wiki formatting:

Short Hacks

User:Pieper:differ

Web Services Links

http://www.xfront.com/REST-Web-Services.html

http://wiki.opengarden.org/REST/REST_for_the_Rest_of_Us

Python windows build notes

  • Upgrade solution files
../../../Slicer3-build/Slicer3 --launch ../../python-build/PCbuild/python.exe setup.py --verbose install

mt -manifest mtrand.pyd.manifest "-outputresource:mtrand.pyd;2"

Summer 2009 Projects by Category

Applications/Analysis

  1. Measuring Alcohol Stress Interaction (Vidya Rajgopalan Virginia Tech)
  2. Lupus Lesion Segmentation (Jeremy Bockholt MRN)
  3. Atlas to CT Registration in Trigeminal Neuralgia (Marta Peroni PoliMI)
  4. Stochastic Tractography to study VCFS and Schizophrenia (Sylvain Bouix BWH)
  5. Meningioma growth simulation (Andrey Fedorov BWH)
  6. Linking atlas data with ontologies of brain morphology and function (Ion-Florin Talos BWH)
  7. MRSI Module (Bjoern Menze MIT)
  8. 4D Imaging (Perfusion, Cardiac, etc.) (Junichi Tokuda BWH)
  9. Gated 4D ultrasound reconstruction for Slicer3 (Danielle Pace Robarts Institute)
  10. multi-modality statistical toolbox for MR T1, T2, fMRI, DTI data (Diego Cantor Robarts Institute)

Segmentation

  1. White Matter Lesion segmentation (Minjeong Kim UNC)
  2. Skull Stripping (Snehasish Roy JHU)
  3. EM Segment (Sylvain Jaume MIT, Nicolas Rannou BWH)
  4. FastMarching for brain tumor segmentation (Andrey Fedorov BWH)
  5. New Level Set Framework in ITK (Arnaud Gelas, Harvard Medical School)
  6. Tubular Surface Segmentation in Slicer (Vandana Mohan, Georgia Tech)
  7. The Vascular Modeling Toolkit in 3D Slicer (Daniel Haehn BWH)
  8. Cortical Thickness Pipeline (Clement Vachet UNC)
  9. Automatic brain MRI processing pipeline (Marcel Prastawa Utah)
  10. Segmentation of Knee Structures (Harish Doddi Stanford)
  11. Spherical Mesh Diffeomorphic Demons Registration (Luis Ibanez Kitware)
  12. HAMMER Registration (Guorong Wu UNC)

Registration

  1. BSpline Registration in Slicer3 (Samuel Gerber Utah)
  2. Registration reproducibility in Slicer3 (Andrey Fedorov BWH)
  3. Prostate Registration Slicer Module (Yi Gao, Georgia Tech)
  4. Slicer 3 registration (Andrew Rausch BWH PNL)
  5. EPI Correction in Slicer3 (Ran Tao Utah)
  6. 2d/3d Registration (and GPGPU acceleration) for Radiation Therapy (Tina Kapur BWH)

IGT

  1. Transrectal Prostate Biopsy (Andras Lasso Queen's)
  2. Prostate Robotics (Junichi Tokuda BWH)
  3. Liver Ablation in Slicer (Ziv Yaniv Georgetown)
  4. Demo of Neuronavigation using Brainlab, Slicer3, BioImage Suite (Haiying Liu BWH)
  5. 3D GRASE (Scott Hoge BWH)
  6. Using RTHawk to Implement MR Navigation (Ben Schwartz BWH)
  7. Integration of Flexible Surgical Instrument Modeling and Virtual Catheter with Slicer (Jayender Jagadeesan BWH)
  8. Integration of stereo video into Slicer3 (Mehdi Esteghamatian Robarts Institute)

Radiotherapy

  1. Adaptive Radiotherapy - Deformable registration and DICOMRT (Greg Sharp MGH)
  2. Adaptive Radiotherapy for Head,Neck, and Thorax (Ivan Kolesov GATech)
  3. 2009_Summer_Project_Week_Cone_Beam_backprojection(Zhou Shen U Michigan)
  4. 2009_Summer_project_week_3d_Deformable_alignment(Dan McShan U Michigan)
  5. accelerate calculation for LDR seeds (Jack Blevins Acousticmed)

Informatics

  1. XNAT user interface improvements for NA-MIC (Dan Marcus WUSTL)
  2. XNAT File System with FUSE (Dan Marcus WUSTL)
  3. XNAT integration into Harvard Catalyst i2b2 framework (Yong Harvard)
  4. GWE-XNAT Integration (Marco Ruiz UCSD)
  5. GWE Results Browser Improvements (Marco Ruiz UCSD)

Diffusion

  1. Functional Analysis of White Matter in Whole Brain Clustering of Schizophrenic Patients (Doug Terry BWH)
  2. Slicer module for the computation of fibre dispersion and curving measures (Peter Savadjiev BWH)
  3. DWI/DTI QC and Preparation Tool: DTIPrep (Zhexing Liu UNC)
  4. DTI digital phantom generator to create validation data sets - webservice/cmdlin module/binaries are downloadable from UCLA (Nathan Hageman UCLA)
  5. Fluid mechanics tractography and visualization (Nathan Hageman UCLA)

CUDA

  1. Developing interactive stochastic tractography using CUDA (Julien de Siebenthal BWH)
  2. acceleration of parallel real time processing of strain and elasticity images for monitoring of ablative therapy (Clif Burdette Acousticmed)

Python

  1. Using ITK in python (Steve Pieper BWH)
  2. Accelerating python with cython: application to stochastic tractography (Julien de Siebenthal BWH)
  3. Taking advantage of multicore machines & clusters with python (Julien de Siebenthal BWH)
  4. Deferring heavy computational tasks with Slicer python (Julien de Siebenthal BWH)

Slicer Internals

  1. VTK 3d Widgets in Slicer3 (Nicole Aucoin BWH)
  2. Updates to Slicer3 Colors module (Nicole Aucoin BWH)
  3. Orthogonal Planes in Reformat Widget (Michal Depa MIT)
  4. Slicer3 Informatics Workflow Design & XNAT updates for Slicer (Wendy Plesniak BWH)
  5. Slicer3 Extension Manager (Katie Hayes BWH)
  6. IAFE Mesh Modules - improvements and testing (Curt Lisle Knowledge Vis)

Execution Model

  1. Plug-in 3D Viewer based on XIP (Lining Yang Siemens Research)
  2. Extension of the Command Line XML Syntax/Interface (Bennett Landman)
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