Curator Dashboard

Computer program that provides a graphical user interface for fMRI researchers to easily and efficiently design their blocked experiments. The computer program POBE calculates the optimal number of subjects and the optimal scanning time for user specified experimental factors and model parameters so that the statistical efficiency is maximised for a given study budget. POBE can also be used to determine the minimum budget for a given power. Furthermore, a maximin design can be determined as efficient design for a possible range of values for the unknown model parameters.

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• SciCrunch
• 13 years ago - by Anonymous

A multichannel capable tool for probabilistic inhomogeneity correction implemented as both a standalone command line tool and a Slicer3 module.

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• SciCrunch
• 13 years ago - by Anonymous

A lightweight software library to manage complex multi-stage data processing. A pipeline is a collection of jobs, i.e. Matlab or Octave codes with a well identified set of options that are using files for inputs and outputs. To use PSOM, the only requirement is to generate a description of a pipeline in the form of a simple Matlab / Octave structure. PSOM then automatically offers the following services: * Run jobs in parallel using multiple CPUs or within a distributed computing environment. * Generate log files and keep track of the pipeline execution. These logs are detailed enough to fully reproduce the analysis. * Handle job failures : successful completion of jobs is checked and failed jobs can be restarted. * Handle updates of the pipeline : change options or add jobs and let PSOM figure out what to reprocess !

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• SciCrunch
• 13 years ago - by Anonymous

A pipeline for small RNA-seq data analysis.

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• SciCrunch
• 13 years ago - by Anonymous

A self-contained virtual machine that can be executed on a common laptop or desktop, enabling the Pipeline to run virtually anywhere. Neophytes to the Pipeline can have their own private server running in minutes, software engineers and workflow designers can use the PNVE as a sandbox, and those without access to grid computing facilities can now take full advantage of the Pipeline processing environment.

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• SciCrunch
• 13 years ago - by Anonymous

Software application for millisecond accurate experimental control for cognitive neuroscience, psychology and linguistics research. Presents text, images, sounds, movies, self-paced reading trials and rating scales. An integrated Python scripting API is available. Joystick and microphone response are available. Supports button boxes from PST, Cedrus, fORP and custom built response boxes. Paradigm can detect fMRI triggers through serial and parallel ports. Includes sample experiments that implement many of the most popular experiment designs., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 13 years ago - by Anonymous

This package contains a software implementation for joint label fusion and corrective learning, which were applied in MICCAI 2012 Grand Challenge on Multi-Atlas Labeling and finished in the first place. Joint label fusion is for combining candidate segmentations produced by registering and warping multiple atlases for a target image. Corrective learning can be applied to further reduce systematic errors produced by joint label fusion. In general, corrective learning can be applied to correct systematic errors produced by other segmentation methods as well.

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• SciCrunch
• 13 years ago - by Anonymous

From state of the art post-processing and visualization software for BOLD, Diffusion / DTI, and Perfusion / DCE imaging to fMRI hardware for audio and visual stimulation, eye tracking, and patient response collection, they provide products and solutions that define the field of functional MR imaging. They are dedicated to bringing the most advanced neuro-imaging tools to market while making functional MRI programs easy to implement. Through collaboration with research and clinical teams from both academic and medical centers, MR system manufacturers, and third party vendors they develop and manufacture hardware and software solutions that meet the needs of very experienced centers while developing training programs to make fMRI easy to adopt for more novice users. Their products are used around the world by researchers and clinicians alike.

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• SciCrunch
• 13 years ago - by Anonymous

NITRC-wide community facilities: Forums, Wiki, Tracker, and News.

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• SciCrunch
• 13 years ago - by Anonymous

A SPM and MATLAB-based software package for statistical analysis of near-infrared spectroscopy (NIRS) signals. Based on the general linear model (GLM), and Sun's tube formula / Lipschitz-Killing curvature (LKC) based expected Euler characteristics, NIRS-SPM not only provides activation maps of oxy-, deoxy-, and total-hemoglobin, but also allows for super-resolution activation localization. Additional features, including a wavelet-minimum description length detrending algorithm and cerebral metabolic rate of oxygen (CMRO2) estimation without hypercapnia, were implemented in the NIRS-SPM software package., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 13 years ago - by Anonymous

A nice sign of bias field correction (nonuniformity) in medical images. This tool is fast and efficient. Technical details can be found at http://zheng.vision.googlepages.com/biasCorrection_miccai09_Zheng.pdf

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• SciCrunch
• 13 years ago - by Anonymous

A scientific visualization application written to display and edit complex, three-dimensional geometric models and scalar, time-based data associated with those models such as high resolution EEG, MEG, and ECG.

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• SciCrunch
• 13 years ago - by Anonymous

A non-invasive, long-range eye tracking system for use in the fMRI environment. Some features of the system include: * Elaborate faraday shielding and fiber optics to avoid noise in high-field magnets. * Includes stimulus presentation software ?Experiment Center? and is compatible with 3rd party products such as ?Presentation? by NeuroBS. * Utilizes mirror box customized for large field of view. * Includes powerful analysis software ?BeGaze2? for graphical and statistical analysis of eye movements. * Includes fixation, saccade and blink detection, and area-of-interest based statistics * Real-time data available via digital or analog output

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• SciCrunch
• 13 years ago - by Anonymous

An infrastructure for managing of diverse computational biology resources - data, software tools and web-services. The iTools design, implementation and meta-data content reflect the broad NCBC needs and expertise (www.NCBCs.org).

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• SciCrunch
• 13 years ago - by Anonymous

An interactive environment for multimodal biosignal data processing and analysis in the fields of clinical research and life sciences. It is the most comprehensive package to analyze non-invasive and invasive brain-, heart- and muscle-functions and dysfunctions. It includes many functions such as support vector machines, event-related ECG, support for P300 and SSVEP/SSSEP BCIs, zero class detection for BCIs, compressed spectral array, minimum energy, and more! g.BSanalyze consists of a base version for data import, visualization, transformation and pre-processing and has several dedicated toolboxes. The package comes with many sample biosignal data-sets, including P300, SSVEP, motor imagery, CSP BCIs, Tilt-Table, EPs, multi-unit activity, CFM, and ERD/ERS.

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• SciCrunch
• 13 years ago - by Anonymous

A Java applet tool for DT-MRI processing. It opens Diffusion-Weighted MRI datasets from user's computer and performs very efficient tensor field estimation using parallel threaded processing on user's browser. No installation is required. It runs on any operating system that supports Java (Windows, Mac, Linux,...). The estimated tensor field is guaranteed to be positive definite second order or higher order and is saved in user's local disc. MATLAB functions are also provided to open the tensor fields for your convenience in case you need to perform further processing. The fanDTasia Java applet provides also vector field visualization for 2nd and 4th-order tensors, as well as calculation of various anisotropic maps. Another useful feature is 3D fiber tracking (DTI-based) which is also shown using 3d graphics on the user's browser.

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• SciCrunch
• 13 years ago - by Anonymous

fNIR Imager 1100 is a new generation portable functional near-infrared (fNIR) imaging research tool capable of monitoring brain?s hemodynamics and thereby the cognitive state of the subject in natural environments. Neuroimaging Solution for Natural Environments: * fNIR is the only stand-alone and field-deployable technology able to determine localized brain activity. * fNIR can be readily integrated with other physiological and neurobehavioral measures that assess human brain activity, including eye tracking, pupil reflex, respiration and electrodermal activity. fNIR can also complement other techniques. * Studies have shown a positive correlation between a participant's performance and fNIR responses as a function of task load. * It has also been shown that fNIR can effectively monitor attention and working memory in real-life situations.

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• SciCrunch
• 13 years ago - by Anonymous

Software toolbox containing many kinds of kits that you may be interested in during fMRI data analysis. This toolbox is a homebrew kits built during practical ASL(arterial spin labeling) based Cerebral Blood Flow (CBF) data analysis. Meanwhile, this toolbox is also compatible with BOLD data analysis. Everyone would find something useful for their own data analysis! This toolbox is run and tested on SPM8 with MATLAB 7.6.0(R2008a) under the Linux OS. Theoretically, most of the functions (except the menu1&2 which are specially designed for the Batch Editor of SPM8) of this toolbox should be compatible with SPM5 and should also work smoothly under the Windows OS. Feel free to give feedback to authors if you encounter any bugs or problems. Senhua Zhu Center for functional Neuroimaging, University of Pennsylvania 3 W.Gates Bldg, 3400, Philadelphia, PA (19104), United States Email: zshtom@gmail.com ; senhua@mail.med.upenn.edu QQ group number (QQ?): 60524357 Google group: https://groups.google.com/d/forum/fmri-grocer

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• SciCrunch
• 13 years ago - by Anonymous

QTL analysis based on imputed dosages/posterior_probabilities.

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• SciCrunch
• 13 years ago - by Anonymous

An EEG toolbox developed to help users with 3 specific types of data and problems: simulatenous EEG-fMRI recording, continuous EEG scoring (e.g. sleep) and handling (visualisation, cutting, power spectrum, etc.) multi-channel recording of spontaneous EEG. The toolbox is written in Matlab and is specifically compatible with the BrainAmp family of EEG recorders (from BrainProducts GmbH) Three other data formats are now also supported: the edf "European Data Format", exported raw-EGI data (from Electrical Geodesics, Inc.) and the BCI2000 format.The results are directly compatible with SPM8 and are saved with SPM8 EEG data format.

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• SciCrunch
• 13 years ago - by Anonymous