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ActiveTab
ActiveTab
Active tab is the currently selected viewing tab at the top of the Workbench Window. The Overlay and Features Toolboxes provide options for viewing that apply only to the Active tab. 


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Brainordinate
Brainordinate
Brainordinate is a brain location that can be is specified by either a surface vertex (node) or a volume voxel.  Brainordinates include grayordinates (gray-matter vertices or voxels) and whiteordinates (white matter voxels).  CIFTI files (see below) contain a list of brainordinates and can handle combined surface/volume representations. 

 

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CIFTI
CIFTI
CIFTI file is a new file format that stores data from surfaces (vertices) and volumes (voxels) concurrently in a single file comprising a listed set of brainordinates.  The volume component of a  A CIFTI file can be contain multiple non-overlapping volume components with different structures, where each volume component is any selected list of voxels (e.g., only subcortical gray-matter left thalamus voxels) that .  These components need not conform to cuboidal or fill the entire grid of ‘N x M x O’ volumetric dimensions.  A CIFTI file can also include multiple surface components with different structures (most commonly, the left and right cerebral cortex), but the surface geometry is not specified in the CIFTI file (commonly, the geometry is in a separate GIFTI surface file). See http://www.nitrc.org/projects/cifti/ for a detailed exposition of the CIFTI-2 file format. 

CIFTI files are consistent with based on the NIFTI-2 file format and by convention therefore have the a filename extension ending in .nii.   Workbench  Workbench currently supports many types of CIFTI files for dense time , including dense scalar (*.dscalar.nii), dense data series (*.dtseries.nii) and , dense connectomes connectome (*.dconn.nii), and dense label (*.dlabel.nii), where the term 'dense' refers to having a value at each listed brainordinate (as opposed to a parcellated file such as *.ptseries.nii, where each value is shared across many brainordinates). Files in the now-deprecated CIFTI-1 format are still supported by Workbench and can be converted to CIFTI-2 using wb_command -cifti-convert -version-convert.

 

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ConnectomeDB
ConnectomeDB
ConnectomeDBwill be is the web-accessible database that will handle for organizing and distributing all HCP data modalities (MR images, MEG/EEG, and behavioral data) and will be central to HCP data mining.  Once operational, ConnectomeDB will be   ConnectomeDB is accessible from any web browser (see URL below) and also in an internal browser within Workbench using the DB button in the Tools section of the Toolbar. (See IntraDB for Phase I HCP data access.)

 

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AnchorDeformedDataFileDeformedDataFile Deformed data file is a file that has been operated on by a deformation map file, for instance when registering it from a source to a target surface.  By default, the expression ‘deformed_’ is prepended to the file name and to the column name after applying a deformation map, but this can be modified as specified by the user or within the deformation map filehttps://db.humanconnectome.org) and linked from the Connect Menu within Workbench.

 

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DenseTimeSeries
DenseTimeSeries
Dense Time Series file contains BOLD activation maps for each timepoint in the resting state fMRI time series. A dense time series can be viewed as single maps at given timepoints or as a movie of sequential timepoint maps using the animate function in the Toolbox Connectivity tab.  A dense time series can also contain columnar brainordinate data of any kind (e.g. each column may contain an ICA component, a task activation map, etc.).

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DenseConnectome
DenseConnectome
Dense Connectome refers to connectivity matrix files that contain correlations between every surface or volume brainordinate and every other surface or volume ordinate in our model of the brain. These files are REALLY big (~30 GB for current resolution). Therefore, they are kept in the HCP database ConnectomeDB, which can access these large files as needed to view connectivity maps of interest.  Dense connectomes can also be asymmetric, such as a structural connectivity matrix between grayordinates (all gray matter strucures) and whiteordinates (all white matter structures).

 

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FeaturesToolbox
FeaturesToolbox
Features Toolboxrefers to the section of the Workbench Window that allows the user to select and set display attributes for Features such as Borders and Foci in the current Active Viewing tab. 

 

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GIFTI
GIFTI
GIFTI file is a file format for surface representations that is supported by all major brain mapping visualization platforms (http://www.nitrc.org/projects/gifti).

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Grayordinate
Grayordinate
Grayordinate Grayordinate is a brain gray matter location that can be represented by a surface vertex (node) or a volume voxel. 

 

AnchorIntraDBIntraDBIntraDB is the web-accessible HCP database for Phase I data.  IntraDB is accessible from any web browser (see URL below) and also in an internal browser within Workbench—click the DB button in the Tools section of the Toolbar.  To get an account for IntraDB, go to:  https://intradb.humanconnectome.org and register for access  (currently WU-Minn HCP consortium members only).  Grayordinates represent a subset of all brainordinates.

 

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Menubar
Menubar
Menu bar refers to the gray bar containing pulldowns (menus) of program-wide functions located at the very top of the screen (Mac) or at the top of the Workbench Window (PC and Linux). Menu items include File, View, Data, Surface, Volume, Window and Help.

 

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NIFTI
NIFTI
NIFTI file (*.nii and *nii.gz) is a standard file format for volumetric data that is widely used in neuroimaging.  The original NIFTI-1 file format was based on 16-bit signed integers and was limited to 32,767 in each dimension. The NIFTI-2 format (http://www.nitrc.org/forum/message.php?msg_id=3738) is based on 64-bit integers and can handle very large volumes and matrices.

 

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Parcellation
OverlayToolbox
Parcellation
OverlayToolbox
ParcellationOverlay Toolboxrefers to the division section of the cerebral cortex and subcortical volume into regions that share functional or structural properties.

 

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Workbench Window that allows the user to set the data to be displayed on the structure in the active tab. 

 

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Scene
Scene
Scene refers to the current state (settings and files being visualized) within Workbench. You can save these settings globally in a scene file, which allows you to re-access your current Workbench session at a later time. By reopening a saved scene file, a user can “pick up where they left off” when they reopen Workbench.

 

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SpecFile
SpecFile
Specification File (commonly called “Spec File”) is a file used to organize a set of data files (such as volume, label, and metric files) to be loaded into Workbench.


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SplashScreen
SplashScreen
Splash Screen is the first window that opens upon launching Workbench that serves as a title page and shortcut for opening Spec files. It contains a list of Spec files in your current path and those that have been recently opened that can be selected and opened in one step. It also contains links to the HCP website and Twitter feed.  

 

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SurfaceMontage
SurfaceMontage
Surface Montage is a viewing mode in which lateral and medial views of both left and right hemispheres are shown in a single viewing area and can be rotated in tandem for a full surface view of the brain.

 

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TabMontage
TabMontage
Tab MontageTile Tabs is a setting that displays the images from all of the tabs you have open in the current Workbench Window in one Viewing Area.  All the surfaces and/or volumes displayed in Tab Montage can still be manipulated with the mouse controls (rotate, zoom, pan).  This option allows you to view and compare multiple structures and datasets at once. Access tab montage from the ViewScreen menu, or through the keyboard shortcut: command + M (Mac) or control + M (PC/Linux). 

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Whiteordinate
Whiteordinate
Whiteordinate Whiteordinate is a brain white matter location.  It is generally represented by a list of white matter voxelsvoxel, though in principle, it can also be represented by a surface vertices vertex (nodes).node). Whiteordinates represent a subset of all brainordinates.  In a CIFTI file, a list of whiteordinates need not fill the entire grid of the ‘N x M x O’ volumetric dimensions.

 

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WorkbenchWindow
WorkbenchWindow
Workbench Window refers to the main interface of Workbench, containing the Viewing Tabs, Toolbar, Viewing Area and Toolbox. In PC/Linux, the Workbench Window also includes the Menu bar. More than one Workbench Window can be opened at one time, either by selecting New Window from the File menu or from selections made from the Window menu.

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