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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.

(last updated: Aug 10, 2019)

Physical Resource or Software Tool Software

426 Results - per page

Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
MRI CVPRResource, segmentation software, image analysis software, data processing software, software application, software resource, image processing softwareTools processing MRI data with a number of techniques from cvpr conference, including segmentation, matching, features, and classification.magnetic resonance, mri, segmentation, matching, feature, classificationSCR_001684(MRI CVPR, RRID:SCR_001684)listed by: NITRCLast checked upnlx_155662
cmrepResource, software resource, image analysis software, data processing software, software applicationA set of deformable modeling algorithms for shape analysis and structure-specific normalization. Applications of cm-reps include structure-specific fMRI analysis, DTI analysis, and structural brain mormagnetic resonanceSCR_009434(cmrep, RRID:SCR_009434)listed by: NITRCLast checked upnlx_155535
Baby Brain ToolkitResource, image analysis software, data processing software, software application, software resource, software toolkit, image processing softwareSoftware 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.computational neuroscience, magnetic resonance, fetus, brain, development, mriSCR_009440(Baby Brain Toolkit, RRID:SCR_009440)ERClisted by: NITRCPMID:23036854Last checked upnlx_155584
Create DWI AtlasResource, software resource, software toolkitThis 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 Atlasmagnetic resonanceSCR_009455(Create DWI Atlas, RRID:SCR_009455)listed by: NITRCLast checked upnlx_155601
False Discovery Rate WeightedResource, software resource, software applicationSimple and efficient, this application performs the Weighted False Discovery Rate procedure of Benjamini and Hochberg (1997) to correct for multiple testing. The good think is that you can test virtually any number of p-values (even millions) obtained with any test-statistics for any data set. The bonus is that you can assign a-priori weights to give a better chance to those variables that you deem important. In practice, this procedure is powerful only with a relatively small number of p-values.magnetic resonanceSCR_009473(False Discovery Rate Weighted, RRID:SCR_009473)listed by: NITRCLast checked upnlx_155620
vmtk in 3DSlicerResource, segmentation software, image analysis software, data processing software, software application, software resource, software toolkitA series of modules which enable functions of the Vascular Modeling Toolkit ( in 3D Slicer ( The functionality includes vessel enhancement filtering, level set segmentation, centerline computation, network extraction and branch splitting.dicom, macos, microsoft, modeling, magnetic resonance, nrrd, posix/unix-like, python, segmentation, visualization, win32 (ms windows), windowsSCR_002579(vmtk in 3DSlicer, RRID:SCR_002579)Vascular Modeling Toolkit related to: 3D Slicer, Insight Segmentation and Registration Toolkit, listed by: NITRCLast checked downnlx_155981
ASL spm8Resource, software resourceQuick ASL Wrapper for preprocessing arterial spin labeled (ASL) Data and computing blood flow measurements using UPenn ASL toolbox.magnetic resonanceSCR_008873(ASL spm8, RRID:SCR_008873)related to: ASL data processing tool box, listed by: NITRCLast checked upnlx_155580
COMPAREResource, software resource, software application, image processing software, data processing softwareGeneric classification tool for 3D imagesmagnetic resonanceSCR_000855(COMPARE, RRID:SCR_000855)listed by: NITRCLast checked upnlx_155598
ScribeResource, software resourceScribe encodes papers to populate the BrainMap Databasemagnetic resonance, pet, spectSCR_000423(Scribe, RRID:SCR_000423)used by:, listed by: NITRCLast checked upnlx_155958
Computational Morphometry ToolkitResource, software resource, software toolkit, software applicationA software toolkit for computational morphometry of biomedical images, CMTK comprises a set of command line tools and a back-end general-purpose library for processing and I/O. The command line tools primarily provide the following functionality: registration (affine and nonrigid; single and multi-channel; pairwise and groupwise), image correction (MR bias field estimation; interleaved image artifact correction; EPI unwarping), processing (filters; combination of segmentations via voting and STAPLE; shape-based averaging), statistics (t-tests; general linear model). CMTK is implemented in C++ with parallel processing using POSIX Threads (SMP), OpenMP (SMP), Grand Central Dispatch (SMP), and CUDA (GPU). Supported file formats include Analyze (r/w), NIFTI (r/w), Nrrd (r/w), DICOM (read), BioRad (read). Data exchange with other toolkits, such as ITK, FSL, AFNI, SPM, etc. is thus easily accomplished.reusable library, analyze, anatomic, artifact removal, atlas application, c, c++, console (text based), cygwin, dicom, domain independent, format conversion, image display, image reconstruction, image-to-image, labeling, linear, linux, macos, microsoft, magnetic resonance, nifti-1, nrrd, posix/unix-like, principal component analysis, region of interest, registration, regression, resampling, segmentation, sh/bash, spatial transformation, statistical operation, sunos/solaris, two dimensional display, unix shell, visualization, warping, win32 (ms windows), windows, workflowSCR_002234(Computational Morphometry Toolkit, RRID:SCR_002234)neurodebian listed by: NITRCLast checked upnlx_155536
NeuroPub VisualizerResource, software resource, software application, data visualization software, data processing software, mobile appA NIfTI visualizer for statistical brain images (fMRI, VBM, etc) the iPad. The visualizer displays these images as overlay on the MNI standard brain. You can use it to store all your statistical images from your fMRI / VBM / TBSS studies and visualise them in 2D and 3D. Use NeuroPub as a library for your statistical images. It's the perfect app to bring to meetings, conferences, etc, and show your latest results.magnetic resonance, fmri, vbm, tbssSCR_006797(NeuroPub Visualizer, RRID:SCR_006797)listed by: NITRCLast checked upnlx_155827
JHU Proj. in Applied Medical ImagingResource, software resourceThis project is used for students enrolled in courses using the JIST framework. Content in this CVS is freely available, but it is not intended for any specific purpose.magnetic resonanceSCR_009499(JHU Proj. in Applied Medical Imaging, RRID:SCR_009499)Johns Hopkins University; Maryland; USA related to: JIST: Java Image Science Toolkit, listed by: NITRCLast checked upnlx_155647
MASIMatlabResource, software resourceThis repository stores and provides opportunities for collaboration through Matlab code, libraries, and configuration information for projects in early stage development. The MASI research laboratory concentrates on analyzing large-scale cross-sectional and longitudinal neuroimaging data. Specifically, they are interested in population characterization with magnetic resonance imaging (MRI), multi-parametric studies (DTI, sMRI, qMRI), and shape modeling.magnetic resonance, matlab, population characterization, mri, dti, smri, qmri, shape modelingSCR_009506(MASIMatlab, RRID:SCR_009506)Vanderbilt University; Tennessee; USA listed by: NITRCLast checked upnlx_155655
MagPro Magnetic StimulatorResource, material resource, resourceA complete line of non-invasive magnetic stimulation systems designed for clinical examinations and for research in the areas of neurophysiology, neurology, cognitive neuroscience, rehabilitation and psychiatry.experiment control, hardware, magnetic resonance, response monitoring, stimulus presentation, clinical, neurophysiology, neurology, cognitive neuroscience, rehabilitation, psychiatry, instrument, equipmentSCR_009601(MagPro Magnetic Stimulator, RRID:SCR_009601)listed by: NITRCLast checked upnlx_155803
Task Independent Fluctuations DiscussionResource, software resource, narrative resource, discussion, data or information resourceThe methodology and applications of task independent fluctuation measures including: connectivity maps of fMRI resting state scans, research using EEG/MEG/PET etc, methods to remove non-neural fluctuations, and applications to clinical, information resource, knowledge environment, model, magnetic resonance, other software resource, web environment, fmri, fmri resting state, eeg, meg, pet, non-neural fluctuation, clinicalSCR_009515(Task Independent Fluctuations Discussion, RRID:SCR_009515)listed by: NITRCLast checked upnlx_155677
factory t1 dtiResource, software resource, image analysis software, data processing software, software applicationTools to make easier on using spm, pipedream, dti-tk, and other softwares to analyze t1 or dti images.magnetic resonance, analyze, t1, dtiSCR_009523(factory t1 dti, RRID:SCR_009523)listed by: NITRCLast checked upnlx_155684
FIVResource, data visualization software, software application, data processing software, software resourceA tool for visualizing functional and anatomic MRI data.analyze, dicom, image display, java, linux, macos, microsoft, minc, magnetic resonance, nifti, posix/unix-like, sunos/solaris, visualization, web environment, win32 (ms windows), mriSCR_009575(FIV, RRID:SCR_009575)Washington University School of Medicine in St. Louis; Missouri; USA listed by: NITRCLast checked upnlx_155756
GIFTIResource, software resource, narrative resource, standard specification, data or information resourceGeometry format under the Neuroimaging Informatics Technology Initiative (NIfTI). Basically, it is the surface-file format complement to the NIfTI volume-file format .nii. Programs which support the Gifti format, intended to allow exchange of each others surface files, include: Freesurfer, Caret, BrainVISA, Brain Voyager, CRkit, VisTrails and AFNI.algorithm or reusable library, c, computational neuroscience, information resource, magnetic resonance, os independent, pythonSCR_009579(GIFTI, RRID:SCR_009579)related to: Neuroimaging Informatics Technology Initiative, listed by: NITRCLast checked upnlx_155761
Lumina LP- 400 Response SystemResource, material resource, resourceA reliable patient response system designed specifically for use in an fMRI. Lumina was developed to satisfy the requirements of both the clinical and research fields.experiment control, hardware, magnetic resonance, response monitoring, fmri, clinical, research, instrument, equipmentSCR_009596(Lumina LP- 400 Response System, RRID:SCR_009596)listed by: NITRCLast checked downnlx_155789
SVVResource, data visualization software, software application, data processing software, software resourceSoftware application that has been designed to facilitate rapid and flexible visualization from neuroanatomically segmented results.c, computed tomography, linux, magnetic resonance, nifti, pet, spect, posix/unix-like, rendering, software, surface rendering, visualization, neuroanatomy, surface, volumeSCR_009613(SVV, RRID:SCR_009613)listed by: NITRCLast checked upnlx_155835
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