From CMIC-wiki

Revision as of 01:07, 2 August 2007 Shahrum (Talk | contribs) Software ← Previous diff		Current revision Ucacrpg (Talk | contribs) Seminars and Reading Groups
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	= The CMIC Group =		= The CMIC Group =
	== Administration ==		== Administration ==
-	For any queries regarding the administration of CMIC please contact Dominique Drai on Ext. 31320 betweeen 09:30 and 13:30. Dominique is located in room 4.13	+	For any queries regarding the administration of CMIC please contact Ron Gaston on Ext. 30221. Ron is located in room 3.09 of the Engineering Front Building
	Requests for a Wiki user name and password should be sent to [mailto:R.Gaston@ucl.ac.uk Ron].		Requests for a Wiki user name and password should be sent to [mailto:R.Gaston@ucl.ac.uk Ron].
-	Holiday request form [[Media:leave-form.pdf]]	+	'''PowerPoint Poster templates:'''
		+
		+	A0 Portrait PowerPoint 97/2003 [[Media:CMIC-powerpoint-template-A0-portrait.ppt]].
		+
		+	A0 Landscape PowerPoint 97/2003 [[Media:CMIC-powerpoint-template-A0-landscape.ppt]]. WIKI Media messes up the formatting when uploading the file. Please reposition the CMIC logo to the bottom right hand corner of the poster.
		+
		+
		+
		+	HCMIC Logo vector file: [[Media:cmic-logo.pdf]]
	Room bookings: [http://www.cs.ucl.ac.uk/cgi-bin/roombooking/ CS]		Room bookings: [http://www.cs.ucl.ac.uk/cgi-bin/roombooking/ CS]
	[http://www.ucl.ac.uk/efd/roombooking/ UCL]		[http://www.ucl.ac.uk/efd/roombooking/ UCL]
	[https://internal.medphys.ucl.ac.uk/booking/ Med Phys]		[https://internal.medphys.ucl.ac.uk/booking/ Med Phys]
		+
		+	Voicemail quick reference: [[Media:VoiceMailQR.pdf]] (from Mark White); see [http://www.ucl.ac.uk/efd/telecoms/voicemail/ UCL voicemail page] for official manual, forms etc.
		+
		+	== Funding ==
		+	For the latest funding opportunities: UCL colleagues are encouraged to sign up for the Research Strategy Forum mailing list at https://www.mailinglists.ucl.ac.uk/mailman/listinfo/beams-research-board. The BEAMS research facilitators produce a document each month detailing the funding opportunities that are currently available. These will appear here.
		+
		+	Funding Opportunities August 2011 [[media:BEAMS Sucesses and Opportunities - August 2011 (2).pdf]].
		+
		+	The EPSRC have changed the way they are funding Fellowships. Please see the Faculty of Engineering for more details. Matt Davies, research facilitator for BEAMS, gave a very informative presentation on the changes the EPSRC have introduced. Please follow the links below.
		+
		+	EPSRC Fellowship Briefing (EPSRC slides) [[media:EPSRC Fellowships Briefing August 2011.ppt]].
		+
		+	EPSRC Fellowship Briefing (UCL slides) [[media:EPSRC Briefing Presentation on Fellowships_UCL.ppt]].
		+
		+	For an in-depth guide to EPSRC fellowships please read: [[media:BEAMS Fellowships guide_Early career v1.pdf]].
	== People ==		== People ==
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	== PhD ==		== PhD ==
-	[[PhD Pages]] Information specific to CMIC PhD students.	+	* [[PhD Pages]] Information specific to CMIC PhD students.
		+	* [http://web4.cs.ucl.ac.uk/research/medic/cmic-wiki/index.php/Image:Newstarters.pdf Newstarters] Pdf version of above.
	== Seminars and Reading Groups ==		== Seminars and Reading Groups ==
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	* [[PDE Discussion Group]].		* [[PDE Discussion Group]].
		+
		+	* [[Registration Discussion Group]].
	* [http://www.ucl.ac.uk/CFN/activities.html Centre for Neuroimaging Techniques (CNT) seminars].		* [http://www.ucl.ac.uk/CFN/activities.html Centre for Neuroimaging Techniques (CNT) seminars].
	* [http://web4.cs.ucl.ac.uk/research/csml/seminars/ CSML Centre for Statistics and Machine Learning].		* [http://web4.cs.ucl.ac.uk/research/csml/seminars/ CSML Centre for Statistics and Machine Learning].
		+
		+	* [[Image-Guided Intervention Workshops]].
		+
		+	* [[Tomography Interest Group]].
		+
		+	* [[IGI Journal Club]].
	= Software =		= Software =
	Information on software used, (or which could be used) at CMIC.		Information on software used, (or which could be used) at CMIC.
		+	See also the CMIC software development [http://cmicdev.cs.ucl.ac.uk/trac/wiki Trac wiki].
		+	* [[Acell]] Details about Bill Crum's analysis of cell images (Updated August 2007).
		+	* [[Boost Libraries]]
	* [http://www.cs.ucl.ac.uk/research/medic/camino/ Camino] Software package for analysis and reconstruction of Diffusion MRI data, tractography and connectivity mapping.		* [http://www.cs.ucl.ac.uk/research/medic/camino/ Camino] Software package for analysis and reconstruction of Diffusion MRI data, tractography and connectivity mapping.
-	* [http://cmicdev.cs.ucl.ac.uk/trac/ vtkCmic] Mark and David's classes for registration etc.	+	* [[dcmtk]] a collection of libraries and applications implementing large parts the DICOM standard.
-	* [[Fluid Registration]] Details about Bill Crum's fluid implementation and related tools.	+	* [[FFTW]] C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST).
-	* [[Matlab]] Numerical linear algebra software, with toolboxes for image processing, stats, optimisation, etc.	+	* [[FLTK]] Fast Light Toolkit
-	* [http://www.vtk.org VTK] C++ visualisation classes (some sort of interface to OpenGL).	+	* [[Fluid Registration]] Details about Bill Crum's fluid implementation and related tools (Updated August 2007).
-	* [http://www.itk.org/ Insight Toolkit] (ITK) C++ imaging and image processing, registration, algorithms classes.	+	* [[FSL]] Toolbox/library for functional and structural neuroimaging analysis, written in C/C++. Popular tools include FLIRT, BET, and FAST.
		+	* [[FreeSurfer]] Cortical surface extraction, sub-cortical structure segmentation and inter-subject registration (FreeSurfer includes '''N3 bias correction''')
		+	* [[giflib]] library for reading and writing gif images.
		+	* [[glpk]] The Gnu Linear Programming Kit
		+	* [[Grace]] Graph drawing program and library
		+	* [[GraphicsMagick]] Image manipulation software for common computer graphics image formats
		+	* [[gxv, DisplayVectorField2D, DisplayVectorField3D]] GIPL X Viewers. Programs to enable display of up to 3 images and overlayed vector fields.
		+	* [[imlib2]] 'X' image display routines.
		+	* [[Insight Toolkit]] [http://www.itk.org] (ITK) C++ imaging and image processing, registration, algorithms classes.
	* [[ITKplusplus|ITK++]] C++ Daniel and Julia's image processing and registration classes		* [[ITKplusplus|ITK++]] C++ Daniel and Julia's image processing and registration classes
		+	* [[latex2html]] Perl program to convert latex to html [http://www.latex2html.org]
		+	* [[Matlab]] Numerical linear algebra software, with toolboxes for image processing, stats, optimisation, etc.
		+	* [[niftkAffine]] NifTK intensity based rigid or affine registration
		+	* [http://cmicdev.cs.ucl.ac.uk/trac/browser/trunk/matlab Matlab Function Repository] Matlab Functions for Image Processing and File I/O.
		+	* [[ParaView]] is an open-source, multi-platform data analysis and visualization application.
		+	* [[Perl OpenOffice::OODoc]] OpenOffice package for Perl - enables generation of Office documents, such as slideshows from Perl scripts.
		+	* [[SPM]] Matlab toolbox for segmentation, spatial normalisation, and voxel-wise statistical analysis of brain images.
		+	* [[SSH]]
		+	* Subversion Version Control Software: [http://svnbook.red-bean.com/en/1.5/index.html Online Manual] and [[Media:Svn-book.pdf|PDF Book]].
		+	* [[TetGen]] "A Quality Tetrahedral Mesh Generator and Three-Dimensional Delaunay Triangulator."
	* [http://math.nist.gov/tnt/ TNT] C++ templated matrix classes.		* [http://math.nist.gov/tnt/ TNT] C++ templated matrix classes.
	* [[TOAST]] Martin and Simon's finite element solvers and tools in C++.		* [[TOAST]] Martin and Simon's finite element solvers and tools in C++.
-	* [[SPM]] Matlab toolbox for segmentation, spatial normalisation, and voxel-wise statistical analysis of brain images.	+	* [[Virtual Network Computing (VNC)]] Desktop sharing system, for remote working, demos etc.
-	* [[FSL]] Similar toolbox/library written in C/C++. Popular tools include FLIRT, BET, and FAST.	+	* [[VTK]] C++ visualisation classes (some sort of interface to OpenGL).
-	* [[FreeSurfer]] Cortical surface extraction, sub-cortical structure segmentation and inter-subject registration	+	* [http://cmicdev.cs.ucl.ac.uk/trac/ vtkCmic] Mark and David's classes for registration etc.
-	* (FreeSurfer includes '''N3 bias correction''')	+	* [[xfig]] Drawing program for the X Windows system.
-	* [[gxv, DisplayVectorField2D, DisplayVectorField3D]] GIPL X Viewers. Programs to enable display of up to 3 images and overlayed vector fields.	+	<br>
		+	* [[Misc.]] General (not medical-imaging) tools, e.g. Bibliography software, PDF tools, etc.
	* Plus see the list at [[Structural-Neuro#Useful_Neuro_Software]].		* Plus see the list at [[Structural-Neuro#Useful_Neuro_Software]].
		+
		+	==Image File Formats ==
		+
	* [[Image File Formats]] Software available to read and manipulate image file formats and '''DICOM''' images in particular.		* [[Image File Formats]] Software available to read and manipulate image file formats and '''DICOM''' images in particular.
-	* [[FAQ]]
	* [[Nifti]]		* [[Nifti]]
-	* [[Misc.]] General (not medical-imaging) tools, e.g. Bibliography software, PDF tools, etc.	+	* There are a number of fairly complete descriptions of deformation and image formats used at CMIC on the [http://cmicdev.cs.ucl.ac.uk/trac Trac wiki].
-	* [[SSH]]	+	* [http://www.dclunie.com/medical-image-faq/html Medical Image FAQ]
-	* [[Virtual Network Computing (VNC)]] Desktop sharing system, for remote working, demos etc.	+
-	* [[New CMIC Wiki]] Discussion on a new CMIC Wiki / web pages	+	= Conference Proceedings =
		+
		+	A directory containing the electronic copies of the conference proceedings can be found at: /cs/research/cmic/conf-proc.
		+
		+	= [[FAQ]] =
		+
		+	= [[Discussion]] =
		+	Discussion on a new CMIC Wiki / web pages
	= Projects =		= Projects =
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	Pages for specific projects at CMIC.		Pages for specific projects at CMIC.
		+	* [[Mammo Group|Breast Cancer Imaging]]
	* [[CMIC Cluster]] Sunfire Cluster - Comic100		* [[CMIC Cluster]] Sunfire Cluster - Comic100
	* [[Moving Liver]]		* [[Moving Liver]]
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	* [[UCLSiemensMRphysics]] UCL Siemens MR Physics user group.		* [[UCLSiemensMRphysics]] UCL Siemens MR Physics user group.
	* [[UCL Imaging Software]] Discussion on possible coordination of UCL Medical Imaging Software.		* [[UCL Imaging Software]] Discussion on possible coordination of UCL Medical Imaging Software.
		+	* [[CMIC IGI Projects]] Project updates and agendas for the IGI management meetings.
	= Science-div =		= Science-div =
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-	Please see [http://meta.wikipedia.org/wiki/MediaWiki_i18n documentation on customizing the interface]	+	Please see [http://meta.wikimedia.org/wiki/Help:Editing documentation on customizing the interface]
	and the [http://meta.wikipedia.org/wiki/MediaWiki_User%27s_Guide User's Guide] for usage and configuration help.		and the [http://meta.wikipedia.org/wiki/MediaWiki_User%27s_Guide User's Guide] for usage and configuration help.

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Current revision

This is the UCL Centre for Medical Image Computing (CMIC) wiki. The official CMIC webpage is here.

Contents 1 The CMIC Group 1.1 Administration 1.2 Funding 1.3 People 1.4 PhD 1.5 Seminars and Reading Groups 2 Software 2.1 Image File Formats 3 Conference Proceedings 4 FAQ 5 Discussion 6 Projects 7 Science-div 7.1 Useful links 7.2 Ethics 7.3 Deadlines 8 Undergraduate and MSc Projects 9 Postgraduate 10 Reading Material

The CMIC Group

Administration

For any queries regarding the administration of CMIC please contact Ron Gaston on Ext. 30221. Ron is located in room 3.09 of the Engineering Front Building

Requests for a Wiki user name and password should be sent to Ron.

PowerPoint Poster templates:

A0 Portrait PowerPoint 97/2003 Media:CMIC-powerpoint-template-A0-portrait.ppt.

A0 Landscape PowerPoint 97/2003 Media:CMIC-powerpoint-template-A0-landscape.ppt. WIKI Media messes up the formatting when uploading the file. Please reposition the CMIC logo to the bottom right hand corner of the poster.

HCMIC Logo vector file: Media:cmic-logo.pdf

Room bookings: CS UCL Med Phys

Voicemail quick reference: Media:VoiceMailQR.pdf (from Mark White); see UCL voicemail page for official manual, forms etc.

Funding

For the latest funding opportunities: UCL colleagues are encouraged to sign up for the Research Strategy Forum mailing list at https://www.mailinglists.ucl.ac.uk/mailman/listinfo/beams-research-board. The BEAMS research facilitators produce a document each month detailing the funding opportunities that are currently available. These will appear here.

Funding Opportunities August 2011 media:BEAMS Sucesses and Opportunities - August 2011 (2).pdf.

The EPSRC have changed the way they are funding Fellowships. Please see the Faculty of Engineering for more details. Matt Davies, research facilitator for BEAMS, gave a very informative presentation on the changes the EPSRC have introduced. Please follow the links below.

EPSRC Fellowship Briefing (EPSRC slides) media:EPSRC Fellowships Briefing August 2011.ppt.

EPSRC Fellowship Briefing (UCL slides) media:EPSRC Briefing Presentation on Fellowships_UCL.ppt.

For an in-depth guide to EPSRC fellowships please read: media:BEAMS Fellowships guide_Early career v1.pdf.

People

People at CMIC. Please enter your phone numbers, email address, room number, and whatever else at this address. There's also a staff page on the external website which is useful for finding contact details.

PhD

• PhD Pages Information specific to CMIC PhD students.
• Newstarters Pdf version of above.

Seminars and Reading Groups

Information on seminars at CMIC.

• ImPr Pages Informal seminars on image processing.

• CMIC seminars. Seminars on research at CMIC and outside.

• CMIC Journal Club Information on the new CMIC Journal Club.

• Diffusion reading group.

• PDE Discussion Group.

• Registration Discussion Group.

• Centre for Neuroimaging Techniques (CNT) seminars.

• CSML Centre for Statistics and Machine Learning.

• Image-Guided Intervention Workshops.

• Tomography Interest Group.

• IGI Journal Club.

Software

Information on software used, (or which could be used) at CMIC. See also the CMIC software development Trac wiki.

• Acell Details about Bill Crum's analysis of cell images (Updated August 2007).
• Boost Libraries
• Camino Software package for analysis and reconstruction of Diffusion MRI data, tractography and connectivity mapping.
• dcmtk a collection of libraries and applications implementing large parts the DICOM standard.
• FFTW C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST).
• FLTK Fast Light Toolkit
• Fluid Registration Details about Bill Crum's fluid implementation and related tools (Updated August 2007).
• FSL Toolbox/library for functional and structural neuroimaging analysis, written in C/C++. Popular tools include FLIRT, BET, and FAST.
• FreeSurfer Cortical surface extraction, sub-cortical structure segmentation and inter-subject registration (FreeSurfer includes N3 bias correction)
• giflib library for reading and writing gif images.
• glpk The Gnu Linear Programming Kit
• Grace Graph drawing program and library
• GraphicsMagick Image manipulation software for common computer graphics image formats
• gxv, DisplayVectorField2D, DisplayVectorField3D GIPL X Viewers. Programs to enable display of up to 3 images and overlayed vector fields.
• imlib2 'X' image display routines.
• Insight Toolkit [1] (ITK) C++ imaging and image processing, registration, algorithms classes.
• ITK++ C++ Daniel and Julia's image processing and registration classes
• latex2html Perl program to convert latex to html [2]
• Matlab Numerical linear algebra software, with toolboxes for image processing, stats, optimisation, etc.
• niftkAffine NifTK intensity based rigid or affine registration
• Matlab Function Repository Matlab Functions for Image Processing and File I/O.
• ParaView is an open-source, multi-platform data analysis and visualization application.
• Perl OpenOffice::OODoc OpenOffice package for Perl - enables generation of Office documents, such as slideshows from Perl scripts.
• SPM Matlab toolbox for segmentation, spatial normalisation, and voxel-wise statistical analysis of brain images.
• SSH
• Subversion Version Control Software: Online Manual and PDF Book.
• TetGen "A Quality Tetrahedral Mesh Generator and Three-Dimensional Delaunay Triangulator."
• TNT C++ templated matrix classes.
• TOAST Martin and Simon's finite element solvers and tools in C++.
• Virtual Network Computing (VNC) Desktop sharing system, for remote working, demos etc.
• VTK C++ visualisation classes (some sort of interface to OpenGL).
• vtkCmic Mark and David's classes for registration etc.
• xfig Drawing program for the X Windows system.

• Misc. General (not medical-imaging) tools, e.g. Bibliography software, PDF tools, etc.
• Plus see the list at Structural-Neuro#Useful_Neuro_Software.

Image File Formats

• Image File Formats Software available to read and manipulate image file formats and DICOM images in particular.
• Nifti
• There are a number of fairly complete descriptions of deformation and image formats used at CMIC on the Trac wiki.
• Medical Image FAQ

Conference Proceedings

A directory containing the electronic copies of the conference proceedings can be found at: /cs/research/cmic/conf-proc.

FAQ

Discussion

Discussion on a new CMIC Wiki / web pages

Projects

Pages for specific projects at CMIC.

• Breast Cancer Imaging
• CMIC Cluster Sunfire Cluster - Comic100
• Moving Liver
• Diffusion MRI
• LSQR reconstruction of MRI
• CMIC Logo (images for your talks etc)
• Structural-Neuro
• UCLSiemensMRphysics UCL Siemens MR Physics user group.
• UCL Imaging Software Discussion on possible coordination of UCL Medical Imaging Software.
• CMIC IGI Projects Project updates and agendas for the IGI management meetings.

Science-div

Useful links

• ISMRM ISMRM British Chapter
• MathWorld
• E-Journals (UCL)
• Abramowitz and Stegun Math Tables
• Numerical Recipes

Ethics

• Self plagiarism (with Splat tool)
• CAFAS, academic freedom in uk

Deadlines

• Deadlines - Details of upcoming conference deadlines.

Undergraduate and MSc Projects

UGprojectDA on Parallel computing for the reconstruction of magnetic resonance images.

Postgraduate

• Maths for Engineer Summer School

• MSc Medical Image Computing (publicly readable)

Reading Material

Reading Material (publicly readable)

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Please see documentation on customizing the interface and the User's Guide for usage and configuration help.