to open a subject’s T1-weighted scan and then superimpose the hippocampal subfields segmentations, type in:

freeview

•             Select File,  Load Volume (or use the Load button on the left toolbar)

•             Select the T1.mgz file in the subject’s “mri” directory

•             Open another volume (File,  Load Volume, or use the Load button [green +])

•             Select the left (or right) hippocampal segmentations i.e. lh.hippSfLabels-T1.v10.mgz

•             Change the Color Map (on the left toolbar) to “Lookup Table”. The hippocampal subfields will now appear as different colours.

•             Click the box “Show existing labels only”

•             To render the subfields without the T1 scan in 3D, unclick the T1 scan (upper left), and then click “Show as isosurface in 3D view”

•             In the “Range” boxes, type in 203 and 226 (these are the subfield label numbers). Press Enter.

•             Select the 1x1 box (top toolbar)

•             Right-click anywhere on the 3D image and select Show Slice Frames (3D View), the frames will now be removed

•             Slide the mouse whilst holding down the right mouse button to zoom, the left button to rotate, and the middle button to move the object.

•             To generate a smoother rendering, slide the “Smooth iterations” bar to the right (maximum value is 20).

Regards,

Jerome