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Statistical method and software for conducting image- and coordinate-based meta-analysis of neuroimaging studies investigating differences in brain activity (e.g. BOLD response in fMRI, metabolism in PET) or structure (e.g. gray matter volume in VBM, voxel-based or TBSS white matter fractional anisotropy in DTI, etcetera).

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• SciCrunch
• 13 years ago - by Anonymous

A Matlab demo for constructing a neuro-anatomical shape complex atlas from 3D MRI brain structures, based on the paper Ting Chen, Anand Rangarajan, Stephan J. Eisenschenk and Baba C. Vemuri, Construction of a Neuroanatomical Shape Complex Atlas from 3D MRI Brain Structures. In NeuroImage, Volume 60, Page 1778-1787, 2012

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• SciCrunch
• 13 years ago - by Anonymous

A free volume processing segmenting tool that combines a flexible manual interface with powerful image processing and segmentation algorithms. Users can explore and label image volumes using slice windows and 3D volume rendering.

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• SciCrunch
• 13 years ago - by Anonymous

An MRI-based atlas of normal adult human brain anatomy, generated by template-free nonrigid registration from images of 24 normal control subjects. The atlas comprises T1, T2, and PD weighted structural MRI, tissue probability maps (GM, WM, CSF), maximum-likelihood tissue segmentation, DTI-based measures (FA, MD, longitudinal and transversal diffusivity), and two labels maps of cortical regions and subcortical structures. The atlas is provided at 1mm isotropic image resolution in Analyze, NIFTI, and Nrrd format. We are also providing an experimental packaging for use with SPM8.

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• SciCrunch
• 13 years ago - by Anonymous

Software to identify motifs, conserved regions, in DNA or protein sequences.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13, 2026. Server that allows you to explore a set of abstracts derived from a MEDLINE search. The system gives you the main associations between the words in groups of abstracts. Then, you can select a subset of your abstracts based on selected groups of related words and iterate your analysis on them. The only input needed is a set of abstracts (in one of the currently accepted input formats) or a definition of how to obtain them. XplorMed is recommended for cases in which you do not know exactly what are you expecting to find. Your interests may be modified by the results obtained, or you may want to inquire new questions as the analysis develops. Also, the results may suggest you additional words that should be used to expand your query in MEDLINE (e.g., unexpected abbreviations of a protein name, or synonyms of a disease).

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• SciCrunch
• 14 years ago - by Anonymous

X-ALD database initiated July 1999 by Hugo W. Moser, M.D. and Stephan Kemp, Ph.D. The primary aims of the database are: to catalogue and facilitate the analysis of X-ALD mutations; to provide background information on X-ALD; to provide links to X-ALD patient organizations; and to help with contacting and finding (local) X-ALD health care professionals. The purpose of the X-linked adrenoleukodystrophy database is to provide general educational information about X-ALD.

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• SciCrunch
• 17 years ago - by Anonymous

Online word processor for scientific and scholarly papers. Write, share, cite, comment, export, and track changes of articles in one place.

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• SciCrunch
• 13 years ago - by Anonymous

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