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| | <pre> | | <pre> |
| | | | |
| − | " Steve Pieper's VIM preferences
| + | " Steve Pieper's VIM preferences |
| − |
| + | |
| − | set nocompatible
| + | set nocompatible |
| − | source $VIMRUNTIME/vimrc_example.vim
| + | source $VIMRUNTIME/vimrc_example.vim |
| − | source $VIMRUNTIME/mswin.vim
| + | source $VIMRUNTIME/mswin.vim |
| − | "behave mswin
| + | "behave mswin |
| − | "
| + | " |
| − | behave xterm
| + | behave xterm |
| − |
| + | |
| − | set wildmode=longest,list
| + | set wildmode=longest,list |
| − |
| + | |
| − | set clipboard=unnamed
| + | set clipboard=unnamed |
| − |
| + | |
| − | set softtabstop=2
| + | set softtabstop=2 |
| − | set expandtab
| + | set expandtab |
| − | set tabstop=2
| + | set tabstop=2 |
| − | set shiftwidth=2
| + | set shiftwidth=2 |
| − | set autoindent
| + | set autoindent |
| − | set showmatch
| + | set showmatch |
| − | set laststatus=2
| + | 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 |
| | | | |
| − | set matchpairs+=<:> " To match arguments of templates
| + | " cycle through tags with control right/left |
| − | set cinoptions={1s,:0,l1,g0,c0,(0,(s,m1 " ITK/VTK style indenting
| + | map <C-Right> :tn |
| − |
| + | map <C-Left> :tp |
| − | 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
| |
| | | | |
| | </pre> | | </pre> |
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| | | | |
| | 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). | | 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). |
| − | | + | <pre> |
| | @echo off | | @echo off |
| | | | |
| Line 72: |
Line 72: |
| | chdir C:\cygwin\bin | | chdir C:\cygwin\bin |
| | | | |
| − | set CYGWIN=binmode tty ntsec
| + | rxvt -fn courier -e /bin/bash --login -i |
| − |
| + | </pre> |
| − | rxvt -e /bin/tcsh -l | |
| − |
| |
| − | REM bash --login -i
| |
| − | | |
| − | <br /> | |
| | | | |
| | == tcsh aliases == | | == tcsh aliases == |
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| | | | |
| | mt -manifest mtrand.pyd.manifest "-outputresource:mtrand.pyd;2" | | mt -manifest mtrand.pyd.manifest "-outputresource:mtrand.pyd;2" |
| − |
| |
| − | == 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)
| |
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
rxvt -fn courier -e /bin/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"
