Unless there is a glitch in the DICOM toolbox, or if you flip the
images using (e.g.) Display, or if the defaults.analyze.flip has
been changed at any time, the left side of the brain should appear
on the left in the lower left panel when you hit the Display button.
Note that if the image is rotated by 180 degrees, then the left
may appear on the right.
If there really is a problem, then it would help to know if the data
are from Siemens mosaic or not. Also, do you get the same problem
if the data are not from mosaic DICOM files? For example, can
your fMRI data be coregistered with your anatomical data without any
additional left-right flipping?
NEVER MESS WITH THE FLIP DEFAULT. IT SHOULD BE SET ONCE FOR YOUR
LAB, AND KEPT AT THAT VALUE.
Best regards,
-John
> I have experienced a similar confusing event lately:
> > The orientation of the images I get from our scanner is R=L.
>
> Same here (we use a Siemens Sonata).
>
> > Did I misunderstand the function of the .flip parameter, or would it be
> > recommendable to flip all images immediately as I get them from the
> > scanner, and set the .flip parameter in SPM to 0 ?
>
> That was my intention here, using a locally written scipt. However, I
> have NOT even normalized the images and still seem to have a flip (or a
> subject whose language is right-dominant and whose left finger is
> controlled by the left brain...)
>
> Could this be a glitch in the DICOM toolbox, which I used in this
> instance? My understanding was that there should be NO flipping during
> converting from DICOM to spm in the spm2-DICOM toolbox. Is there, or
> could there be in special situations? This may also relate to Thomas's
> problem, hence my quick jumping ship...
> Any comments appreciated!
--
Dr John Ashburner.
Functional Imaging Lab., 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
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