> My question is: I just spent my weekend setting crosshair to approximate
> AC-PC line for structural images and use HDR to save the new origin. Then
> I used 'reorient' option of the 'Display' to save the pitches, rolles and
> yaws that I peformed in order to put the images into T1template position.
> The question: do the .mat files, created during 'reorientation' function
> contain the new origin voxels I have saved using HDR edit? If not, how can
> I make sure that SPM uses the origin I want to set during spatial
> normalisation?
Providing the images did not have .mat files before you reoriented the images
using the Display button, then the .mat files should contain the new origins.
If a .mat file doesn't exist, then the headers are read, and origins (accurate
to the nearest voxel) and voxel sizes are used to re-create what the .mat
file probably would have said. Therefore, if one of these images is rotated,
then the "virtual" mat file would have been read, a rotation applied, and then
the results saved to the .mat file. However, if you changed the origin field
in the .hdr of an image that already had a .mat file, then you were wasting your
time.
> Finally, if yes to all the above, can the images I edited
> this way and the .mat files created be used in SPM2b?
Yes. SPM2b will read SPM99 .mat files.
Best regards,
-John
> I've just read this exchange (below) on the archive (one of the links that
> John has attached) and would like to ask a question re: HDR edit and .mat
> files in SPM99.
> ---------------------------------------------------------------------------
>- -------------------------------------
>
> > I'm afraid I'm not the spatial transformations expert, but it seems
> > you just need one piece of information: Once SPM99 creates a .mat file
> > for an image, the Analyze header is *never* considered except to
> > obtain the image dimensions. So if you have .mat file, it doesn't
> > matter what the Analyze header origin says.
>
> This is true for the origin and voxel sizes, but not the image dimensions
> and scalefactor (see
> http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0212&L=spm&O=A&P=9159 ,
> and note that it was Darren Weber who has a header edit utility, and not
> Darren Gitelman - see
> http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0211&L=spm&P=R21025&I=-3 ).
>
> ---------------------------------------------------------------------------
>- ------------------------------------------
>
--
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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