FMRLAB: a Matlab toolbox for fMRI data analysis
What is FMRLAB?
FMRLAB is a Matlab toolbox for fMRI data analysis using Independent Component Analysis (ICA). It provides an integrated environment to manage, process and analyze fMRI data in a single framework so that users can complete the analysis without switching between software. In addition, it provides an interactive Matlab graphic user interface (GUI). All the necessry processes to apply ICA to fMRI data and review its results can be run from the graphic interface. The FMRLAB processing flow is straightforward. Custom analyses can be performed with Matlab scripts using the FMRLAB functions and data structure.
Why FMRLAB?
Since fMRI data analysis is a complex enterprise, including digital image processing, statistical analysis and data visualization, an integrated framework combining processing elements is desired eagerly by users in the neuroimaging community. Recently, large number of software tools for data analysis and visualization have been developed for this purpose. However, most of these tools use model-based statistical methods which assume that the users know the hemodynamic response (HR) for their paradigm in advance and can specify a reasonable HR model. Often, however, accurate or reasonable response HR models are unavailable. An alternative data-driven method, infomax ICA (McKeown et al., 1998), does not require that an a priori HR model, instead deriving HRs of spatially indendent components of the entire data set from the higher-order statistics of the data themselves.
FMRLAB is a toolbox running under Matlab containing necessary components for data-driven fMRI data analysis using the highly reliable infomax ICA algorithm (Bell & Sejnowski, 1995), normalized (Amari, 1999), extended (Lee, Girolami and Sejnowski, 1999) and automated by Makeig et al. FMRLAB has been developed under Matlab 6.1 running on Red Hat Linux.
Caution: FMRLAB is a toolbox written and released for neuroimaging research purposes only. FMRLAB, or data obtained from FMRLAB, should not under any circustances be used for clinical purposes.
FMRLAB Features
- Graphic user interface
- Flexible data importing
- Interactive data plotting
- Computationally efficient
- Defined FMRI data structure
- Independent component browser
- Smooth, transparent component exporting and spatial normalization process
- Interface with other software for further analysis or visualization.
- SPM-style component plots (MIP, 2-D slice overlay and 3-D)
Learn more on the FMRLAB Home Page
Popularity: 1% [?]
iso2mesh: a 3D surface and volumetric mesh generator for matlab/octave
Filed under: Biotecnology, CAD, Computational Geometry, Graphics, Medicine
- iso2mesh is a matlab/octave-based meshing toolbox. It can create 3D tetrahedral finite element (FE) mesh from iso-surfaces and 3D binary volumetric images such as segmented MRI/CT scans.
- iso2mesh is an open-source software developed by [Qianqian Fang] at the [Photon Migration Lab], [Martinos Center for Biomedical Imaging], [Massachusetts General Hospital (Harvard Medical School)].
- A sibling project, metch – a mesh registration toolbox, is also hosted with this website.
Learn Qianqian’s other projects
- [Ask a question], check reply
- Publications involving iso2mesh
- [Verdict on iso2mesh]
- Frequently Asked Questions
Learn more on: http://iso2mesh.sourceforge.net/cgi-bin/index.cgi
Popularity: 1% [?]
Bioelectromagnetism Matlab Toolbox: working with EEG/ERP and MRI images
Taken from: http://eeg.sourceforge.net/
License
This toolbox is released under the GNU General Public License (GPL, see http://www.gnu.org/licenses/gpl.html). This is a copyleft license, which means you have the freedom to use, distribute and modify the code, but only on the condition that you must pass on this freedom. You can integrate this code into proprietary packages, but you must do so according to this rule. That is, some parts of your proprietary package will not have this freedom, but those parts derived from this code must retain that freedom. You must use, distribute and develop the code herein in accordance with the GPL.
EEG Features
Firstly, this is not a signal processing toolbox. Of course, once the data is loaded, there are many matlab functions available for data processing, but few of them are integrated into a GUI interface here. At present, there are no specific functions for processing raw EEG, such as filtering, averaging, etc. For examples of signal processing tools, see the matlab signal processing toolbox and the links below, especially EEGLAB.
This toolbox has been developed to facilitate quick and easy import, visualisation and measurement for ERP data. The toolbox can open and visualise ERP averaged data (Neuroscan, ascii formats), 2D/3D electrode coordinates and 3D cerebral tissue tesselations (meshes). All the features can be explored quickly and easily using the example data provided in the toolbox. The GUI interface is simple and intuitive. The following lists the features already available and some items that could be developed.
ERP Visualisation
- ERP data can be read and plotted as a time series
- Automated or GUI entry of ERP epoch/sampling etc. parameters
- Interactive, precise measurement of ERP waveform values
- Interactive ERP peak detection and plotting/measurement
- Interactive ERP topographic mapping
Data Import/Export Support
- Neuroscan EEG formats (.avg,.eeg,.cnt)
- Neuroscan electrode formats (.tri, .3dd ascii)
- EMSE electrode and mesh formats (.elp/.wfr/.reg)
- FreeSurfer mesh formats (.tri/.asc/.surf/.curv/etc)
- BrainStorm formats
- All data is stored internally in one large, convenient data structure (p), which is available from the matlab workspace.
Topographic Mapping
If the electrode position data is available or adapted from the standardized electrode positions available, the toolbox can generate topographic maps. There are various topography options, including 2D/3D surface mapping with various controls for contour mapping, scaling, and colour maps. If a scalp tesselation is available, the toolbox can load and visualise the ‘mesh’ and interpolating from the electrodes onto the mesh (only when they are already coregistered – the functions for coregistration are in early stages of development).
- standardized extended 10/20 electrode coordinates available
- example realistic geometry, with 124 channel electrode coordinates and associated scalp/skull/cortex tissue meshes from MRI volume provided
- latency selection for topographic mapping based on single values, either entered manually or interactively selected
- animation of topographic maps
- automatic or user-defined amplitude scales
- various color or bw topographic maps (linear or polynomial color scales)
- contour topographic mapping, with automatic or user-defined intervals or numbers of contours specified (rudimentary at the moment – needs refinement)
- Printing or saving graphics files (various formats)
- 3D rotation and left,right,front,back views of 3D topographic maps
The following graphic illustrates 3D scalp topography (with interpolation from 124 electrodes onto a scalp mesh). As of May 2002, the methods are integrated with the GUI interface (they are available in the mesh_laplacian.m and mesh_laplacian_interp.m functions). Many thanks to Robert Oostenveld for assistance in validating these functions.
Data Transforms/Analysis
- Identification/replacement of bad electrodes
- ERP peak detection for all electrodes
- ERP peak detection for regions of electrodes
MRI Features
There are useful functions to load and visualize MRI volumes in Analyze format (or the Freesurfer COR- format and GE Signa files). The Analyze avw* functions have been developed to carefully handle the orientation and implement a strict interpretation of the original Analyze 7.5 specification. This specification is available here in two very informative pdf documents:
If you need to, use the orient option in the avw* functions to handle different image orientations, but read the above documents and this discussion on the issue first (you will be wise in no time).
Also, when working with format conversions, consider these enlightening notes from Mark Jenkinson!
It is expected these MRI functions, together with mesh functions, will provide the opportunity to visualize mesh overlays with MRI volumes. It is also creates an avenue for conversion of MRI volumes. There are some MRI processing functions freely available for matlab, some of them are bundled into the CVS archives, but none are integrated into GUI interfaces yet.
For further MRI processing functions, see the matlab image processing toolbox, the SPM toolbox for matlab, and the FSL tools (in c/c++ with source code available).
System Requirements – Development Platform
The development of this matlab toolbox is in its infancy. It is not very clear what the system requirements are, although matlab 6+ is required. I understand from one report that the toolbox GUI does not work under matlab 5.x, but many command line functions should be OK. For most ERP plotting, the toolbox creates about 4-8Mb of data in the workspace and GUI. For more elaborate mesh plotting and interpolation, the toolbox can create up to 40Mb of workspace data (probably that much again in the GUI itself).
The toolbox has been developed on matlab 6.x on a windows platform. I have noticed some minor problems with mesh plotting and interpolation on systems without OpenGL graphics.
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