Re: [Freesurfer] ERROR: mpr2mni305 failed, see transforms/talairach_avi.log

mri_convert -iks 1 --conform ga_2010.nii 001.mgz

will create an image where the z direction is 1mm. but the orientation will still be wrong, since it was missing from the header (or incorrect). orient_mri can be used to rotate it, but one cannot know whether left or right is correct.

n.

On Mon, 2011-05-16 at 21:35 -0300, Pedro Paulo de Magalhães Oliveira Junior wrote:

The images are: 0.5 x 0.5 x 1.0

Can mri_convert fix it or should I edit the Nifti header?

2011/5/16 Nick Schmansky nicks@nmr.mgh.harvard.edu PPJ,

    Hi,

    mri_info /space/incoming/ga_2010.nii

    shows that the image is 0.5 x 0.5 x 0.5.  but when viewing in
    freeview
    or tkmedit, the brain seems 'squashed', as if there is a slice
    gap.  do
    you know the details of how this was acquired?

    N.



    On Mon, 2011-05-16 at 17:49 -0300, Pedro Paulo de Magalhães
    Oliveira

    Junior wrote:
    > I'm having this error in the recon-all
    >
    >
    > #--------------------------------------------
    > #@# Talairach Mon May 16 16:38:01 EDT 2011
    > /usr/local/freesurfer/subjects/GAGRICOLA/mri
    >
    >
    >  talairach_avi --i orig.mgz --xfm
    transforms/talairach.auto.xfm
    >
    >
    > ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
    >
    >
    > I've uploaded to the ftp at surfer.nmr.mgh.harvard.edu the
    > talairach_avi.log, the orig.mgz (as ppj_orig.mgz) and the
    original
    > nifti image as ga_2010.nii
    >
    >
    > Any hints?
    >
    >
    >
    >

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