> Thanks. This means that spm_dicom_convert flip the dicom image onto the
> SPM right-handed system.
>
> In this case, I suppose that the defaults.analyze.flip should be set to
> zero.
> Am I right ?
Providing that the flip always remains the same, then it should only matter
if you are sharing data with other sites or software. I think most sites
have the flip set to 1. Also, if flip is set to 0, then you are not using
a proper Analyze format. Also note the compatibility issues with spatially
normalised data from SPM99.
The data can be stored in a left- or right- handed co-ordinate system. If
flip is set to 1, then SPM converts from voxels in a left-handed co-ordinate
system (as used by Analyze) into a set of right-handed co-ordinates. If flip
is set to 0, then SPM assumes data are stored using a right-handed system
(as in spatially normalised data in SPM99) and no flipping is done.
The way that spm_dicom_convert works is that the data are stored in the same
order as they are originally reconstructed. The order of the planes is changed
in order to preserve the handedness, and a .mat file is written that stores
the image position and orientation relative to the co-ordinates of the scanner.
The origin is set to be the centre of the magnetic field. This allows saggital
and coronal images to be displayed as if they were transverse. It also means
that if several images were acquired from the same subject, and the subject didn't
move, then the images are in register - even if there is a mixture of different
voxel sizes, orientations etc. It should also help to provide better starting
estimates for spatial normalisation (assuming that the AC is not more than about
5cm from the centre of the field and that there is reasonable head coverage).
Best regards,
-John
> >>Using SPM2b DICOM toolbox, spm_dicom_convert reads raw data from dicom
> >>files in radiological conventions.
> >>Are the output Analyze files still in radiological conventions, or ready
> >>to SPM - neurological conv, in the display ?
> >
> >Assuming there are no bugs in the code, the Display button will show the
> >axial image with the left side of the brain on the left. This should be
> >the same if you acquire coronal or sagittal data (and you show the images
> >in world space). The only exception is if the positioning of the subject
> >is not the same as what is entered into the scanner console. For example,
> >if for some reason the subject lies face down, and the scanner believes
> > that the subject is face up, then the axial image will have the left side
> > shown on the right and the back of the brain shown at the top. If this
> > is the case, then the orientation can be corrected with a rigid-body
> > re-orientation which is simply a matter of entering a series of
> > rotations. No zooming should be done. See
> > http://www.fil.ion.ucl.ac.uk/spm/spm2b.html#Compat for more information.
> >
> >I don't really like the neurological/radiological notation. A better
> > notation is left-handed/right-handed. See section 2.2.3 of
> >http://www.fil.ion.ucl.ac.uk/~john/thesis/chapter2.pdf
--
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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