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SPM  May 2010

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Subject:

Re: Images left-right inverted in SPM

From:

Pouria Mojabi <[log in to unmask]>

Reply-To:

Pouria Mojabi <[log in to unmask]>

Date:

Fri, 28 May 2010 10:46:42 -0700

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (96 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?

-P


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]>
> > >
> > >
> > 
> > 
> > 
> 

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