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Software tool that computes point-based models using a parametric boundary description for the computing of Shape analysis. The point-based models computed with the SPHARM-PDM tool can be used in combination with the also UNC designed statistical tool shapeAnalysisMANCOVA to perform quantitative morphological assessment of structural changes at speci?c locations. Shape analysis has become of increasing interest to the medical community due to its potential to precisely locate morphological changes between healthy and pathological structures.

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• SciCrunch
• 13 years ago - by Anonymous

A matlab-based 3D shape modeling and analysis toolkit, and is designed to aid statistical shape analysis for identifying morphometric changes in 3D structures of interest related to different conditions. SPHARM-MAT is implemented based on a powerful 3D Fourier surface representation method called SPHARM, which creates parametric surface models using spherical harmonics.

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• SciCrunch
• 13 years ago - by Anonymous

A software toolbox that can automatically identify many of the artifact components that are often present in independent component analysis (ICA) of functional MRI (fMRI). The method: * Does not require temporal information about the fMRI paradigm. * Does not require the user to train the algorithm. * Requires only the EPI images (additional acquisition of anatomical images is not required). * Is able to identify a high proportion of artifact-related ICs without removing components that are likely to be of neuronal origin. * Can be applied to resting-state fMRI. * Is automated, requiring minimal or no human intervention.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 09, 2013. Brain Briefings is a newsletter series explaining how basic neuroscience discoveries lead to clinical applications. Brain Briefings is published during the academic year and prepared for a lay audience.

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• SciCrunch
• 15 years ago - by Anonymous

A powerful software for model-based analysis of peripheral psychophysiology (e.g. skin conductance, heart rate, pupil size etc.). General linear modelling and dynamic causal modelling of these signals provide for inference on neural states/processes. SCRalyze includes flexible data import and display, statistical inference and results display and export. Easy programming of add-ons for new data formats, signal channels, and models.

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• SciCrunch
• 13 years ago - by Anonymous

A Problem Solving Environment (PSE) for modeling, simulation and visualization of scientific problems. SCIRun now includes the biomedical components formally released as BioPSE, as well as BioMesh3D. BioMesh3D is a free, easy to use program for generating quality meshes for the use in biological simulations. The most recent stable release is version 4.6.

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• SciCrunch
• 13 years ago - by Anonymous

Software to fit s-reps to segmented anatomic objects, to compute probability distributions on these s-reps, to train and to apply classifiers between two classes of anatomic objects, and to apply hypothesis testing to determine which geometric or physiological features vary significantly between two classes. Software for object segmentation from medical images may also be included. S-reps are skeletal models for anatomic objects especially suited for computing probability distributions from populations of these objects and for providing object-related coordinates for the interior of these objects. They allow classification and hypothesis testing using their geometric features and physiological features derived from medical images. They also allow the definition of shape spaces, probability-based geometric typicality functions, and appearance models used for segmentation or registration. A variety of successful applications to objects in neuroimages have already been performed.

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• SciCrunch
• 13 years ago - by Anonymous

An automatic cortical thickness measurement tool for rat brains. The pipeline consists of four steps: preprocessing to create binary mask and label map, thickness measurement which produces laplacian field and thickness map in order, run particle correspondence followed by statistical analysis resulting in mean thickness color map and t-test result. By running RodentThickness, you will need to fill in informations in a Graphical User Interface, and then compute. You can also run the tool in command line without using the GUI. Using the GUI, you will be able to save or load a dataset file or a configuration file. The tool needs these other tools to work, so be sure to have these installed on your computer: * ImageMath * measureThicknessFilter * GenParaMeshCLP * ParaToSPHARMMeshCLP * ShapeWorksRun * ShapeWorksGroom * SegPostProcessCLP * BinaryToDistanceMap * MeshPointsIntensitysampling

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• SciCrunch
• 13 years ago - by Anonymous

A modified version of the Brain Extraction Tool (BET) that can process rodent brains.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13, 2026. Database aimed at helping laboratory-based bacteriologists make best use of bacterial genome sequence data, with a particular emphasis on comparative genomics. The latest version, xBASE 2.0, now provides comprehensive coverage of all bacterial genomes and features an updated modularized backend and an improved user interface, which includes a taxonomy browser and a powerful full-text search facility. There are 2082 genomes in the database, 1062 complete and 1020 incomplete xSites: * coliBASE - a genome resource for the E. coli research community * campyDB - a genome resource for the Campylobacter research community * MycoDB - a genome resource for the Mycobacteria research community * RhizoDB - a genome resource for the Rhizobia research community * FtBASE - a genome resource for the Francisella research community * ClostriDB - a genome resource for the Clostridiales research community If you use xBASE in your work, please cite: xBASE2: a comprehensive resource for comparative bacterial genomics. Chaudhuri RR, Loman NJ, Snyder LA, Bailey CM, Stekel DJ, Pallen MJ. Nucleic Acids Res. 2008 Jan;36(Database issue):D543-6. Epub 2007 Nov 5.PMID: 17984072 This work is supported by the BBSRC, grant number BBE0111791, awarded to MJP and DJS.

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• SciCrunch
• 16 years ago - by Anonymous

Project to discuss, debate, develop and deploy ontological practices for the fMRI community.

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• SciCrunch
• 13 years ago - by Anonymous

Software application to visualize, segment, and quantify three-dimensional images. Multiple datasets may be loaded, displayed, fused, processed, and quantitatively analyzed simultaneously. Data may be imported from any DICOM-compatible three dimensional imaging modality. Regions-of-interest may be defined using a number of manual, semi-automatic, and automated tools to segment three-dimensional pixel volumes. They may also be imported from and exported to DICOM structure sets. This software has been applied to preclinical and clinical computed tomography (CT), positron emission tomography (PET), single photon emission computed tomography (SPECT), magnetic resonance imaging (MRI), and optical imaging data.

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• SciCrunch
• 13 years ago - by Anonymous

An automatic whole-brain extraction tool for T1-weighted MRI data (commonly known as skull stripping). Whole-brain segmentation is often the first component in neuroimage pipelines and therefore, its robustness is critical for the overall performance of the system. Many methods have been proposed in the literature, but they often: * work well on certain datasets but fail on others. * require case-specific parameter tuning ROBEX aims for robust skull-stripping across datasets with no parameter settings. It fits a triangular mesh, constrained by a shape model, to the probabilistic output of a supervised brain boundary classifier. Because the shape model cannot perfectly accommodate unseen cases, a small free deformation is subsequently allowed. The deformation is optimized using graph cuts.

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• SciCrunch
• 13 years ago - by Anonymous

So far there is a lack for Random Field Theory (RFT) -based multiple comparison correction for surfaces generated in Freesurfer software package. This set of Matlab-based functions can be used for that purpose. They are based on Worsley?s SurfStat toolbox. You also need to have installed Freesurfer software package and included the Freesurfer?s matlab subdirectory in the Matlab?s search path. In addition, this tool implements the RFT-FDR hierarchical correction that can be used for optimizing the amount of smoothing in cortical thickness analyses (Neuroimage 52, 158-171).

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• SciCrunch
• 13 years ago - by Anonymous

A stand-alone MATLAB-based toolkit for the rapid and flexible exploration of Region of Interest (ROI) response waveforms and other signals from across large fMRI datasets. An alpha-release is currently available for use with an example dataset and tutorial.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13, 2026. Computationally oriented experimental laboratory interested in the encoding of auditory information in the cerebral cortex and brainstem, and in the mechanisms of tinnitus and the effect of various drugs (Lidocaine, steroids, anti-oxidants) in relieving noise trauma induced tinnitus. The ferret (Mustela putorius) and the rat serve as their system model. Through chronic implants, they obtain electrophysiological data from awake behaving animals in order to investigate the response properties and functional organization of the auditory system, both in health and after noise trauma that induces tinnitus in rats. Projects: * Response Modulation to Ongoing Broadband Sounds in Primary Auditory Cortex * Neuronal Response Characteristics in the Inferior Colliculus of the Awake Ferret and Rat * Spectro-Temporal Representation of Feature Onsets in Primary Auditory Cortex * Targeting the changes in inferior colliculus induced by tinnitus

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• SciCrunch
• 14 years ago - by Anonymous

The package fmri provides fMRI analysis with R using structural adaptive smoothing methods. They allow smoothing especially at low SNR avoiding the apparent blurring of non-adapative smoothing and thus without reducing the effective spatial resolution.

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• SciCrunch
• 13 years ago - by Anonymous

Software for short read simulating in order to facilitate sequencing-based study designs.

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• SciCrunch
• 13 years ago - by Anonymous

The package dti provides methods for structural adaptive smoothing of diffusion weighted data in the context of the diffusion tensor model. Through its edge preserving properties they reduce data noise without compromizing significant structures.

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• SciCrunch
• 13 years ago - by Anonymous

Slicer3 modules for quantitative diffusion analysis. Modules include tools for clustering fiber tracts, summarizing measures over tract clusters, etc.

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• SciCrunch
• 13 years ago - by Anonymous