In Freeview:
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).
[image: Inline images 1]
Regards,
Jerome
On 15 August 2016 at 06:19, Jacobs H (NP) h.jacobs@maastrichtuniversity.nl wrote:
Hi!
I would like to create a 3D rendering of the hippocampal subfields generated by FreeSurfer (as done in the Iglesias paper). I have tried to do this using Slicer, but the results are not that nice (making a model based on the 1mm mgz file). How were the surfaces in the paper generated? Do you have any suggestions for me on how to do this?
Many thanks
Heidi
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