![]() Bio-Formats– a Java library for reading and writing popular microscopy file formats capable of parsing both pixels and metadata for a large number of formats, as well as writing to several formats (maintained in collaboration with LOCI, ).OMERO: a Java-based server/client system for visualising, managing, and annotating microscope images and metadata.It includes a web browser interface, a threshold segmentation and tracking application (called “findSpots”), a MatLab interface, support for VisBio, LDAP, BioFormats and much more. OME Server: a Perl-based for visualising, managing, and analysing microscope images and metadata.Designed to interact with existing commercial software, all OME formats and software is free! Now available: See the BMAP Software page for more information on software created in the lab.OME is a multi-site collaborative effort among academic labs and a number of commercial entities that produces open tools to support data management for biological light microscopy. Cortical Surface Analyses, Making Meshes, Working with UCFs (from Dr.Simple UNIX Tutorial (foreach loops, etc.).Cortical Thickness (Flat-Mapping) Scripts (Under Construction).Loading and viewing UCFs with ShapeViewer.This protocol describes how to display 3D cortical objects with different cut-out views to show subcortical structures or activation at a particular slice (for fMRI).Preparing Figures for Publications and Presentations Pipelines from our group available for download.Glyphs: Show tensor directional information with glyphs in BrainSuite.Adding Objects to *rgb Data: Adding the 3D objects to your figures showing your DTI colormap data.Creating objects from masks: Use ROI masks to create 3D overlays on DTI data.Working with DTI Data in BrainSuite 2.45.Voxel Based Morphometry Analysis of DTI Data Using T-Tests.Voxel Based Morphometry Analysis of DTI Data Using the General Linear Model.Creating UCF Regions of Interest (ROIs).Running False Discovery Rate (FDR) Correction using R.Finding mean cortical thickness values using R.Running permutations in R with an ROI mask.Mixed Model: Creating p maps using R but modeling for random factors (using an ANOVA).Creating p maps using R (using an ANOVA).Using R statistical analysis software ( ).TBM Longitudinal Jacobians and Analysis (One Sample T-Test).TBM Statistical Analysis (Volume Regression Analysis).Running TBM Processing and Analysis through the LONI Pipeline.Identifying the uncinate fasciculus in DTIStudio using a multiple ROI approach.Identifying the inferior longitudinal fasciculus in DTIStudio using a multiple ROI approach.Identifying the inferior fronto-occipital fasciculus in DTIStudio using a multiple ROI approach.Identifying the fornix in DTIStudio using a multiple ROI approach.Identifying the cingulate gyrus component of the cingulum in DTIStudio using a multiple ROI approach.Identifying the arcuate fasciculus in DTIStudio using a multiple ROI approach.Load DTIStudio Tractography Files in DTIStudio.Shape Analysis Preprocessing (Surface Deformation Scripts).Hippocampus tracing protocol (or download hippo_protocol.doc file).Tracing Subcortical Structures in MultiTracer.Converting an analyze file to a mask using BrainSuite.Skull Stripping in MultiTracer Using the TraceWalker Utility.Masking Protocol (using the MNI Display program).Convert Freesurfer images (.mgz) to anaylze and create Dist Q files.Elastic Surface Warping (Cortical Pattern Matching).Combine sulcal lines to single ucf file.Convert Freesurfer surfaces to Object format.Run Freesurfer on Data using the LONI Pipeline.Download data from Brain Mapping Center.Step by Step Protocol on how to process structural MRI data.Overview of Steps needed to Preprocess data.Load Data in BrainSuite and Shapeviewer.Purple lines denote the thalamus midline. The thalamus is the main part of the diencephalon, and is involved in integrating information from prethalamic inputs to the cerebral cortex. Location of the thalamus in the brain, anterior view.
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