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

1 The CMIC Group
2 Software
- 2.1 Image File Formats
3 FAQ
4 Discussion
5 Projects
6 Science-div
7 Undergraduate and MSc Projects
8 Postgraduate
9 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 4.13

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

PowerPoint Poster templates: A0 Portrait PowerPoint 97/2001 Media:CMIC-powerpoint-template-A0-portrait.ppt.

A0 Landscape PowerPoint 97/2003 Media:CMIC-powerpoint-template-A0-landscape.ppt.

A0 Portrait PowerPoint 2007 Media:CMIC-powerpoint-template-A0-portrait2007.pptx.

A0 Landscape PowerPoint 2007 Media:CMIC-powerpoint-template-A0-landscape2007.pptx.

Holiday request form: Media:leave-form.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.

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.

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.
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.
Matlab Function Repository Matlab Functions for Image Processing and File I/O.
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