> I meet some problems with reorientation of coronal fMRI images. After
> consulting the mailing list, I have understood that coronal fMRI
> acquisitions have to be reoriented in the same way than axial ones, to
> obtain for example sagital view in the upper right with eyes on the left
> in the SPM display window.
>
> Does anybody have met such a reorientation problem? If yes, please,
> could you let me know about pertinent yaw, pitch and roll values to
> reorient our coronal slices in a good way...
There are a few different versions of coronal orientations. How do these
images appear in Display? Is the lower left window a coronal section with
the top of the head at the top of the image and the left on the left? How
are the top two images oriented?
The solution may be as simple as rotating around the X axis by + or - 90
degrees (i.e. + or - pi/2 radians). On the other hand, it may not be.
The easiest way is probably to use trial and error, with various rotations of
pi/2 or pi radians. Alternatively, you could try to figure out what an
affine transformation matrix should look like to get from coronal to
transverse, and then use spm_imatrix to obtain the actual parameters.
To get from coronal to transverse, the x axis of the coronal image may
correspond to the negative of the x axis of the transverse. The y axis of
the coronal image may correspond to the z axis of the transverse, and the z
axis of the coronal corresponds to the y axis of the transverse. Some of
these may need to be negated. e.g.:
xt = -xc
yt = zc
zt = yc
Getting towards affine matrix notation, this is:
xt = -1*xc + 0*yc + 0*zc + 0*1
yt = 0*xc + 0*yc + 1*zc + 0*1
zt = 0*xc + 1*yc + 0*zc + 0*1
1 = 0*xc + 0*yc + 0*zc + 1*1
so, on to Matlab:
M = [-1 0 0 0
0 0 1 0
0 1 0 0
0 0 0 1];
p = spm_imatrix(M)
The results of this is a vector, where the elements are x translation, y
translation, z translation, pitch, roll, yaw, x zoom, y zoom, z zoom and
three shears:
0 0 0 1.5708 0 3.1416 1.0000 1.0000 1.0000 0 0 0
Simply enter these into the left hand panel of the graphics window of
<Display> in order to reorient the image. Be very careful of left-right
orientation.
Best regards,
-John
--
Dr John Ashburner.
Wellcome Department of Cognitive Neurology.
12 Queen Square, London WC1N 3BG, UK.
tel: +44 (0)20 78337491 or +44 (0)20 78373611 x4381
fax: +44 (0)20 78131420
http://www.fil.ion.ucl.ac.uk/~john
mail: [log in to unmask]
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