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NeuroElf - loading anatomical and functional data


This is the initial step when looking at your own dataset, and thus you should try to become acquainted with NeuroElf's interface. There are several ways to load and access files from disk, which will be discussed on this page.

UI-based loading

Given that the file input/output functionality is centralized in one class (function), xff, NeuroElf only requires one menu entry to load the several types of files that are supported:

  • anatomical file types
    • VMR (BrainVoyager QX's VMR format, which is the default for NeuroElf)
    • HDR or NII (Analyze HDR+IMG header or NIftI files)
    • HEAD (AFNI's HEAD/BRIK format)
  • anatomical surface file types
    • SRF (BrainVoyager QX's surface format, currently the only supported format)
  • functional file types
    • NII (4-D NIftI files)
    • VTC (BrainVoyager QX's volume-based timecourse format, which is the default for NeuroElf)
    • FMR (BrainVoyager QX's FMR format)
  • statistical file types
    • VMP (BrainVoyager QX's volumetric map format, which is the default for NeuroElf)
    • HDR or NII (Analyze HDR+IMG header of NIftI files with special SPM-like description)
    • HEAD (AFNI's HEAD/BRIK format, if HEAD indicates statistical content)
    • GLM (BrainVoyager QX's format for general-linear-model results)
  • surface statistical file formats
    • SMP (BrainVoyager QX's surface-based map format, currently the only supported format)

The default behavior in NeuroElf is to show all supported file types, when the File → Open file dialog is invoked. If the filetype selection is changed, this setting is retained for subsequent file opening requests.

Script-based loading

In addition to loading files via the GUI, any object that has been either loaded (e.g. by passing a filename or a filename pattern to xff) or created and correctly populated (by using the 'object = xff('new:type');' syntax, followed by making the appropriate settings) can be added to the GUI's control by using the .Browse method as seen in the following syntax example:

% load object
vmp = xff('*.vmp', 'Please select a VMP to display...');
if isxff(vmp, 'vmp')

Accessing previously loaded objects

In case you need access to an object that has been loaded via the GUI (e.g. to alter some settings that are not exposed through the GUI), you can first get a list of all loaded objects by calling xff without any arguments:

% get root object
xroot = xff;

By displaying the output of this object (or statement, either by not using a semicolon in the above statement or by just typing xroot without semicolon) you will get a list of loaded files, and can then access any of those objects by giving the object number or, for objects that were loaded from disk, the filename:

% access object number 4
object = xroot(4);
% access object with name "subject21.vmr"
vmr21 = xroot('subject21.vmr');

Switching between objects

Once an object is loaded into the NeuroElf GUI, it is accessible via one of the dataset selection dropdowns (see item #1 on the GUI page). In its standard view (when started up), the GUI shows the 3-sections view of volume-based datasets (e.g. VMRs). To switch to surface-based objects, you need to click on the surface button on the right-most toolbar.

Since surface-based maps (SMPs) can only be displayed on matching objects (with the same number of vertices), changing the surface (SRF) object will also change the associated SMP object. This does, however, not affect the display directly. To change the displayed object(s) in the surface view, please (multi-) select the desired entries in the Scenery listbox below the surface.

Undocking the current view

To browse several objects at once, the current view can be “undocked” into a separate window by clicking the undock button (first button in the right-most toolbar). This separate window can be resized to improve visualization depending on the screen size. Any statistical maps displayed will be equally copied to the new window, which also allows to inspect several statistical maps (at the same position) at once, but also allows to browse the same map at different positions (unlinking the browsing position across windows).

neuroelf_gui_-_loading_data.txt · Last modified: 2011/03/17 03:15 by jochen