User:Pieper - Revision history

Pieper: /* cygwin */

2010-10-07T21:32:28Z

cygwin

Pieper: /* vim settings */

2010-09-03T13:11:57Z

vim settings

Pieper: /* Summer 2009 Projects by Category */

2010-06-17T15:05:30Z

Summer 2009 Projects by Category

Pieper: /* Summer 2009 Projects by Category */

2009-06-22T13:55:12Z

Summer 2009 Projects by Category

Pieper: /* Summer 2009 Projects by Category */

2009-06-22T13:51:33Z

Summer 2009 Projects by Category

Pieper: /* Python windows build notes */

2009-06-22T13:50:28Z

Python windows build notes

Pieper: /* vim settings */

2009-04-07T14:59:00Z

vim settings

Pieper: /* vim settings */

2009-04-07T14:57:38Z

vim settings

Pieper: /* vim settings */

2009-02-23T00:05:23Z

vim settings

Pieper: /* Web Services Links */

2009-02-11T13:53:51Z

Web Services Links

@@ Line 66: / Line 66: @@
 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
@@ Line 72: / Line 72: @@
   chdir C:\cygwin\bin
- set CYGWIN=binmode tty ntsec
+  rxvt -fn courier -e /bin/bash --login -i
+</pre>
 == tcsh aliases ==

@@ Line 24: / Line 24: @@
 <pre>
- " Steve Pieper's VIM preferences
+" Steve Pieper's VIM preferences
- set matchpairs+=<:> " To match arguments of templates
+set nocompatible
- set cinoptions={1s,:0,l1,g0,c0,(0,(s,m1 " ITK/VTK style indenting
+source $VIMRUNTIME/vimrc_example.vim
+source $VIMRUNTIME/mswin.vim
- set vb
+"behave mswin
- syntax on
+behave xterm
- " cycle through buffers with control page up/down
- map <C-PageDown> :bn
+set wildmode=longest,list
- map <C-PageUp> :bp
- " delete current buffer with control delete
+set clipboard=unnamed
- map <C-Del> :bd
+set softtabstop=2
- " cycle through tags with control right/left
+set expandtab
- map <C-Right> :tn
+set tabstop=2
- map <C-Left> :tp
+set shiftwidth=2
 </pre>

← Older revision		Revision as of 15:05, 17 June 2010
Line 144:		Line 144:

	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)~~

@@ Line 150: / Line 150: @@
 #[[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_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)
@@ Line 156: / Line 156: @@
 #[[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_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_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)
+#[[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_WML_SEgmentation|White Matter Lesion segmentation]] (Minjeong Kim UNC)
-#[[2009_Summer_Project_Week_Skull_Stripping | Skull Stripping]] (Snehasish Roy JHU)
+#[[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-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)
+#[[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_Spherical_Mesh_Diffeomorphic_Demons_Registration|Spherical Mesh Diffeomorphic Demons Registration]] (Luis Ibanez Kitware)
-#[[2009_Summer_Project_Week_HAMMER_Registration | HAMMER Registration]] (Guorong Wu UNC)
+#[[2009_Summer_Project_Week_HAMMER_Registration|HAMMER Registration]] (Guorong Wu UNC)
 === Registration ===
-#[[BSpline Registration in Slicer3 | BSpline Registration in Slicer3]] (Samuel Gerber Utah)
+#[[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)
+#[[2009_Summer_Project_Week_Slicer3_registration|Slicer 3 registration ]] (Andrew Rausch BWH PNL)
-#[[EPI Correction in Slicer3 | EPI Correction in Slicer3]] (Ran Tao Utah)
+#[[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)
@@ Line 187: / Line 187: @@
 #[[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_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)
@@ Line 198: / Line 198: @@
 #[[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_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)
+#[[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_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_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_XNAT|GWE-XNAT Integration]] (Marco Ruiz UCSD)
-#[[2009_Summer_Project_Week_GWE_Results_Browser | GWE Results Browser Improvements]] (Marco Ruiz UCSD)
+#[[2009_Summer_Project_Week_GWE_Results_Browser|GWE Results Browser Improvements]] (Marco Ruiz UCSD)
 === Diffusion ===
@@ Line 215: / Line 215: @@
 #[[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_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_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)
+#[[2009_Summer_Project_Week_Hageman_FMTractography|Fluid mechanics tractography and visualization]] (Nathan Hageman UCLA)
 === CUDA ===
@@ Line 226: / Line 226: @@
 === Python ===
-#[[Summer2009:Using_ITK_in_python| Using ITK in python]] (Steve Pieper BWH)
+#[[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: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: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)
+#[[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_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)
+#[[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)
+#[[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)
+#[[Summer2009:Extension of the Command Line XML Syntax/Interface|Extension of the Command Line XML Syntax/Interface]] (Bennett Landman)

@@ Line 168: / Line 168: @@
 #[[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)
+#[[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)
@@ Line 177: / Line 177: @@
 === Registration ===
-# [[BSpline Registration in Slicer3 | BSpline Registration in Slicer3]] (Samuel Gerber Utah)
+#[[BSpline Registration in Slicer3 | BSpline Registration in Slicer3]] (Samuel Gerber Utah)
-# [[Summer2009:Registration reproducibility in Slicer|Registration reproducibility in Slicer3]] (Andrey Fedorov BWH)
+#[[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)
+#[[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)
@@ Line 193: / Line 193: @@
 #[[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)
+#[[Integration of stereo video into Slicer3]] (Mehdi Esteghamatian Robarts Institute)
 === Radiotherapy ===
@@ Line 226: / Line 226: @@
 === Python ===
-# [[Summer2009:Using_ITK_in_python| Using ITK in python]] (Steve Pieper BWH)
+#[[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: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: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)
+#[[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_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_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)
+#[[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)
+#[[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)
+#[[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)
+#[[Summer2009:Extension of the Command Line XML Syntax/Interface | Extension of the Command Line XML Syntax/Interface]] (Bennett Landman)

← Older revision		Revision as of 13:50, 22 June 2009
Line 144:		Line 144:

	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)

@@ Line 44: / Line 44: @@
   set showmatch
   set laststatus=2
   set matchpairs+=<:> " To match arguments of templates

@@ Line 22: / Line 22: @@
 The values I use are:
+<pre>
   " Steve Pieper's VIM preferences
@@ Line 67: / Line 66: @@
   map <C-Left> :tp
-<br />
+</pre>
 == cygwin ==

← Older revision		Revision as of 13:53, 11 February 2009
Line 135:		Line 135:

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