Curator Dashboard

Software to: view dicom files and assemble them into 3D volumes. View and convert between Analyze, Nifti, and Interfile. Classify and organize dicoms and 3D volumes using metadata. Search and report on a collection of scans.

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• SciCrunch
• 13 years ago - by Anonymous

A suite of tools for efficient management of neuroimaging project data. Specifically, DFBIdb was designed to allow users to quickly perform routine management tasks of sorting, archiving, exploring, exporting and organising raw data. DFBIdb was implemented as a collection of Python scripts that maintain a project-based, centralised database that is based on the XCEDE 2 data model. Project data is imported from a filesystem hierarchy of raw files, which is an often-used convention of imaging devices, using a single script that catalogues meta-data into a modified XCEDE 2 data model. During the import process data are reversibly anonymised, archived and compressed. The import script was designed to support multiple file formats and features an extensible framework that can be adapted to novel file formats. Graphical user interfaces are provided for data exploration. DFBIdb includes facilities to export, convert and organise customisable subsets of project data according to user-specified criteria.

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• SciCrunch
• 13 years ago - by Anonymous

This package is a set of three slicer modules which together are able to compute a DWI Atlas given a set of DWI''s. The modules included are: # A Groupwise Registration module -> compute''s a deformation field for each DWI, using, for example, FA maps as input # Warp DWI module -> used to warp each DWI using the deformation from (1) # DWI Averager -> used to average the set of warped DWI''s producing the final DWI Atlas

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• SciCrunch
• 13 years ago - by Anonymous

A web enabled data and workflow management system extended from the HID codebase on NITRC specialized for Arterial Spin Labeling data management and analysis (including group analysis) in a centralized manner.

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• 13 years ago - by Anonymous

An open-source C++-based application that allows automatic as well as user-interactive segmentation of the Corpus Callosum. Via a Qt-based graphical user interface, CCSeg also performs semi-automatic segmentation.

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• SciCrunch
• 13 years ago - by Anonymous

A fully automated processing pipeline for cortical analysis of structural MR images at a resolution of up to 400������m, including skull stripping, whole brain segmentation, cortical extraction, surface inflation and mapping, as well as dedicated tools for profile estimation across the cortical thickness. The tools are released as a set of plug-ins for the MIPAV software package and the JIST pipeline environment. They are therefore cross-platform and compatible with a wide variety of file formats.

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• SciCrunch
• 13 years ago - by Anonymous

This project hosts data for CANDI Share Schizophrenia Bulletin 2008 (reference below) as part of the CANDI Neuroimaging Access Point. This set includes preprocessed MRI images and segmentation results of all 4 diagnostic groups (Healthy Controls, N=29; Schizophrenia Spectrum, N=20; Bipolar Disorder with Psychosis, N=19; and Bipolar Disorder without Psychosis, N=35). Frazier JA, Hodge SM, Breeze JL, Giuliano AJ, Terry JE, Moore CM, Kennedy DN, Lopez-Larson MP, Caviness VS, Seidman LJ, Zablotsky B, Makris N. Diagnostic and sex effects on limbic volumes in early-onset bipolar disorder and schizophrenia. Schizophr Bull. 2008 Jan;34(1):37-46.

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• SciCrunch
• 13 years ago - by Anonymous

Software package that allows interoperability between CAMINO and TRACKVIS. CAMINO is a leading software package in DTI processing. The package is from University of College London. TRACKVIS is a tract visualizing utility with capability of visualizing up to and over a million white matter tracts seamlessly. The package is from Massachusetts General Hospital. With increasing efforts on brain connectivity analyses it becomes important to have tools that can allow increased interoperability among different tractography tools. The tools in this package allow conversion of tracts from one format to another in a very effective way with ability to handle over a million tracts.

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• SciCrunch
• 13 years ago - by Anonymous

A small, stand-alone MatLab toolbox that measures sagittal cross-section thickness and area of the human corpus callosum from high-resolution T1 in vivo MR images. C8 takes as input affine normalized white matter segmentations derived from high-resolution (in-plane) T1 images and outputs both regional callosal thicknesses in three different formats and geometrically-defined regional areas in three different configurations. It is a small package that is easily configurable and modifiable and it measures callosa at the rate of several per minute.

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• SciCrunch
• 13 years ago - by Anonymous

An interactive 3D rendering and neuroanatomical analysis package developed for analyzing focal brain lesions and functional brain imaging data (Damasio and Frank, 1991; Frank, Damasio and Grabowski, 1997).

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• 13 years ago - by Anonymous

A collection of tools for MRI T1 brain image segmentation in the Windows environment. It helps construct a complete pipeline with necessary preprocessing and postprocessing procedures besides brainparser, the core program of our fast brain segmentation. The execution of the whole pipeline can be completed in 2 hours with good segmentation results. Execution requires: FSL

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• SciCrunch
• 13 years ago - by Anonymous

Aa brain network visualization tool, which can help researchers to visualize structural and functional connectivity patterns from different levels in a quick, easy, and flexible way.

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• 13 years ago - by Anonymous

A free collection of MRI brain images for testing segmentation algorithms. It is available for download to assess the accuracy, reproducibility and sensitivity of MRI segmentation software. It includes data from infants and adults as well as patients with Alzheimer's disease.

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• SciCrunch
• 13 years ago - by Anonymous

Draw3D is a 3D rendering tool written entirely in VTK-TCL script. It is intended for fast command line rendering and visual inspection of datasets commonly found in medical imaging. It also allows the generation of images for reports or videos. As it is based on pure VTK, it can render whatever VTK can render, and runs wherever VTK can run. Meshinator is a simpler tool that uses VTKs isosurface functions to generate meshes from volumetric data. Please see the wiki for documentation

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• SciCrunch
• 13 years ago - by Anonymous

Commercial organization for hardware and software for neurophysiological research. Provides EEG and ERP amplifier systems, EEG recording caps, Data recording and analysis software, TMS Stimulator for combined EEG/TMS coregistrations and more.

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• SciCrunch
• 13 years ago - by Anonymous

High quality data, open and freely available to everyone to celebrate the diversity of the vertebrate brain. Do you have data that you would like to share? Do not hesitate to contact them! The Brain Catalogue is developed by Florencia Grisanti (Taxidermy Workshop of the Natural History Museum in Paris) and Roberto Toro (Neuroscience Department of the Institut Pasteur). Many of our specimens come from the Vertebrate Brain Collection of the Jardin des Plantes, curated by Marc Herbin, and are scanned at the Institut du Cerveau et de la Moelle (ICM) by Mathieu Santin and Alexandra Petiet, from the CENIR laboratory, with financial and methodological support kindly provided by Olivier Colliot, head of the Cogimage team at the ICM.

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• SciCrunch
• 13 years ago - by Anonymous

A tutorial that took place as part of MICCAI 2010 is the 13th International Conference on Medical Image Computing and Computer Assisted Intervention, September 20-24, 2010 in Beijing, China. See http://www.miccai2010.org/ This project supporedt community outreach and dialog between presenters and audience, both before and after the tutorial session, and is intended to engage the broader community in the deliberations on this important topic. ''Best Practices'' covered software engineering practices as well end-user installation and support practices.

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• SciCrunch
• 13 years ago - by Anonymous

Software toolkit developed for the fbrain project that consists of several image processing tools: image reconstruction, image denoising, image segmentation, tractography etc., for a better understanding of fetal brain development.

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• 13 years ago - by Anonymous

A collection of data processing and image analysis tools for data in BXH or XCEDE format. This includes data format encapsulation/conversion, event-related analysis, QA tools, and more. These tools form the basis of the fBIRN QA procedures and are also distributed as part of the fBIRN Data Upload Scripts.

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• SciCrunch
• 13 years ago - by Anonymous

A novel C++ based application developped at UNC-Chapel Hill that performs automatic brain tissue classification and structural segmentation. AutoSeg is designed for use with human and non-human primate pediatric, adolescent and adult data. AutoSeg uses a BatchMake pipeline script that includes the main steps of the framework entailing N4 bias field correction, rigid registration to a common coordinate image, tissue segmentation, skull-stripping, intensity rescaling, atlas-based registration, subcortical segmentation and lobar parcellation, regional cortical thickness and intensity statistics. AutoSeg allows efficient batch processing and grid computing to process large datasets and provides quality control visualizations via Slicer3 MRML scenes.

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• SciCrunch
• 13 years ago - by Anonymous