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SPM  May 2010

SPM May 2010

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Subject:

Re: Images left-right inverted in SPM

From:

John Ashburner <[log in to unmask]>

Reply-To:

John Ashburner <[log in to unmask]>

Date:

Fri, 28 May 2010 18:58:09 +0100

Content-Type:

text/plain

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Parts/Attachments

text/plain (111 lines)

> Thank you very much for the thorough explanation John.
> so in a proper NIFTI image, you can distinguish radiological vs
> neurological orientation by just using the transformation matrix.
> is that true?

Yes - providing the correct data has been included in the NIfTI headers.
If you wish to check what orientations SPM is assuming, then try typing
the following in MATLAB:

  help spm_orientations

  spm_orientations


Best regards,
-John


> On Fri, 2010-05-28 at 07:56 -0700, John Ashburner wrote:
> > In proper NIfTI images, the orientations are represented by a
> > voxel-to-world mapping, which maps indices of voxels to mm coordinates.
> > SPM can still read the old ANALYZE format images, but if it changes the
> > headers or writes any new images, then the format will be changed to
> > NIfTI.
> >
> > So, if ANALYZE images are used initially, it is up to the users to
> > ensure that SPM is told what the correct orientation of these images is
> > (because any derived images will be in NIfTI format and the NIfTI
> > headers will contain the same information). The
> > spm_flip_analyze_images.m function is ignored once images are in NIfTI
> > format.
> >
> > The Display button allows you to click on different parts of the image,
> > and it shows the mm coordinates (as well as voxel indices). SPM (and
> > other NIfTI compliant packages) assume that the right side of the images
> > has larger (or more positive) x coordinates (in mm).
> >
> > To answer your question, the voxel-to-world mapping is encoded in two
> > ways: sform and qform. SPM primarily uses the sform, and generally sets
> > the qform to have the same values (the exception being those images that
> > have been imported for registration with Dartel). These fields are
> > documented at http://nifti.nimh.nih.gov/nifti-1
> >
> >
> > Occasionally, people notice what they believe to be a left-right mix up
> > when they use the slices option from the results. This is really a
> > feature rather than a problem, as the idea here is to show the original
> > slices in the image. For example, if the images are stored saggitally,
> > then saggital slices are displayed - even if the voxel-to-world mapping
> > indicates the correct transform to axial. Similarly, axial or coronal
> > slices are displayed according to how they are actually stored in the
> > image.
> >
> > Best regards,
> > -John
> >
> >
> > On Thu, 2010-05-27 at 16:26 -0400, [log in to unmask] wrote:
> > > Dear John,
> > >
> > > In what variable of the NIFTI header is this info represented?
> > >
> > > Thanks,
> > > Eric
> > >
> > > Quoting John Ashburner <[log in to unmask]>:
> > >
> > > > SPM assumes that the image orientation is what the data format says it
> > > > is. If the data were to be correctly converted to NIfTI format, then
> > > > SPM should handle them perfectly fine. With the older ANALYZE format,
> > > > left-right orientations are not specified in the headers, so SPM needs
> > > > to be explicitly told what the orientations are.
> > > >
> > > > Best regards,
> > > > -John
> > > >
> > > >
> > > > On Tue, 2010-05-25 at 17:05 +0100, Stephen Paisey wrote:
> > > >> Dear Developers and users,
> > > >> We have imaged rats with a brain lesion on the right hand side on a
> > > >> Bruker scanner using Paravision 5.0. I have then used analyze 9.0
> > > >> to convert the raw bruker files into and img/hdr file pair. The
> > > >> images in analyze 9.0 are displayed the correct way around but when
> > > >> I load them in spm5 (i am using this version for its compatibility
> > > >> with the spmmouse extension) i get an image which has been left
> > > >> right inverted i.e. the lesion is now on the left side of the
> > > >> brain. I can get around this by flipping the image the wrong way
> > > >> around before i read it into spm but this is clearly a bug which
> > > >> could lead to totally wrong experimental results. It is lucky i had
> > > >> non symmetrical rats otherwise i probably wouldn't have spotted
> > > >> the error.
> > > >>
> > > >> Best Regards
> > > >>
> > > >> Stephen
> > > >>
> > > >
> > > > --
> > > > John Ashburner <[log in to unmask]>
> > > >
> > > >
> > >
> > >
> > >
> >
>
>

--
John Ashburner <[log in to unmask]>

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