hiro3

Hiro3 is a visualization program for .img and .nii format (f)MRI data. Short tutorial: load an anatomy and a functional layer via the File menu. Click on the transversal, sagittal and coronal slice views to navigate. Clicking provides a best-guess anatomical label and Brodmann number. These labels are also exported along with other information about centres of activation.

Note that left and right may be switched, on-screen and in labelling! That depends on your analysis sequence; as yet I don't know of a certain, general way to determine that, so be careful. However, negative and positive x values are always as in the XYZ matrix.

Current functionality:

• Multiple overlays can be plotted, each with an independently chosen color scheme and transparency. See the Display menu for the color scheme and transparency dialog.
• Cutoff values for functional overlays can be adjusted without reloading data (press C or use the Data menu). When multiple activation layers are loaded, independent cut-offs can be entered, separated by spaces, in the cut-off dialog. This is especially useful when combining activation data (use a statistical cut-off, e.g. 4) with masked of label-map data (set cut-off to zero).
• Tranversal slices can also be plotted (use the Display menu; an automatic selection of all slices containing activation can be generated, or a selection of z coordinates can be given to choose slices to plot).
• Saves figures as 600 dpi tiffs.
• The program is also an interface to the "blobbify" function for separating and labelling regions of activity surrounding peaks. Blobbify exports a label map and a text file with information about the regions of activation. Blobbify-Borg combines regions if one is surrounded by another by a specified proportion of edge-voxels (0.25 by default).
• Masks and outlines can be created.
• Pressing space toggles between navigation and replace-value mode. Pressing R (or the menu item in the Data menu) allows users to change the value applied to clicked voxels in replace mode.

Requires SPM5 to work.