5. Miscellaneous functions and utilities

This section describes miscellaneous functions and utilities that are included with SPM.

5.1 Display: Interactive orthogonal display of selected image.

Display utilities:

Bottom left panel:

Bottom right panel: contains information about image, its size and space.

5.2 Check Reg(istration)

This allows >1 and <15 images to be displayed at the same time, in the space of the .mat file of the first image selected. This utility is VERY useful for checking coregistration results.

5.3 Render?


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Extracted brain Rendered brain Brain surface

5.4 fMRI/PET

Option to toggle between the PET and the fMRI mode.

5.5. Toolboxes

This option provides access to SPM toolboxes installed in the toolbox subdirectory of the SPM installation directory. A sub-directory must exist under the SPM toolbox directory named after the toolbox. There must be an M-file in this sub-directory whose name ends with the toolbox directory name. E.g. a toolbox for Deformations would contain an M-file called 'spm_Deformations.m' in a subdirectory called Deformations under the SPM toolbox directory.

5.6 Means...


5.7 ImCalc

ImCalc allows basic algebraic calculations to be performed on selected images and the result written as an image. The user must specify the expression to be evaluated in standard matlab form with the selected images referred to in order as i1, i2, i3 ?etc. Logical, relational and trigonometric operators can be used as well as basic arithmetic operators. For information on using these operators in matlab, type 'help arith', 'help relop', 'help slash' and 'help elfun' at the matlab prompt. The user must enter a name for the resulting output image. This will be written to the current working directory.

5.8 HDR edit

HDR edit allows an image header to be edited and applied to selected images. It also allows the creation of image headers. Editing options are:

Set options for editing, then select APPLY to images. A new header file will be written for selected images. This utility is especially useful for adjusting the origin of one or more images to provide a better starting point for coregistration with an image where the origin is very different.

5.9 Help

This provides a graphical user interface for the help files associated with all buttons in the SPM menu window.

5.10 Utils?


5.11 Defaults

This option allows current defaults to be edited. New default settings are reset to SPM defaults when a new SPM session is started.

Printing Options - allows a variety of different printing options to be selected.

Miscellaneous Defaults:

Header Defaults -PET/FMRI - these values are used as the defaults for the HDR edit utility.

The defaults for Realignment, Coregistration, Spatial Normalisation, Statistics -PET/ FMRI were discussed in each of the relevant sections.

Reset All - this reloads the SPM startup defaults from spm_defaults.m.

5.12 Quit

This exits SPM and clears the workspace.