SPM99 Gem 10: Surface Renderings: Rolling your own (w/ blobs!)

Subject: Re: rendering SPM96
From: John Ashburner <john@FIL.ION.UCL.AC.UK&gt
Date: Tue, 20 Feb 2001 16:22:05 +0000
To: SPM@JISCMAIL.AC.UK

SPM96 shows voxels that are considered to be between 5mm in front of and 20mm
behind the surface that is displayed.  This is the same as for the "old style"
rendering of SPM99.

To change this depth, try changing line 131 of spm_render.m from:
        msk = find(xyz(3,:) &lt (z1+20) &amp xyz(3,:) &gt (z1-5));
to something like:
        msk = find(xyz(3,:) &lt (z1+5) &amp xyz(3,:) &gt (z1-5));


I would rather see the rendering done on the brain of either the same
subject that the data were acquired, or on a nice smooth average brain
surface.  Rendering can be done on a smooth average in SPM99, and there
is also the capability of doing the rendering on to the individual subjects
MR.  The rendering in SPM96 is done onto a single subject brain, which can
be quite misleading as it is not the same subject that the data comes
from.  Depths behind the surface are derived from the single subject brain,
which can cause problems as spatial normalisation is not exact.  An activation
that could be on the brain surface may appear a few mm in front of or behind
the single subject brain surface.

Another option within SPM99 is to use the brain extraction feature to
identify the approximate brain surface of a segmented structural image.
This would be saved as surf_*.mat.  A routine similar the one attached
can then be used to render the blobs on to this surface.

Best regards
-John
  

Attached file:fancy_rendering.m

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