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