> Any ideas on what the T1 vs EPI normalization difference is caused by?
This is almost certainly results from distortions of the EPI images,
relative to the T1w. This means that rigid-body registration between
T1w and EPI usually does not result in accurate alignment (try Check
Reg between the coregistered scans). There are various approaches for
achieving more accurate alignment.
1) Acquired fieldmaps. This is the most common approach, but it does
require additional scans to be acquired from the subject. If you
don't collect field maps, then you can't do a field map correction.
See eg. Hutton, Chloe, Andreas Bork, Oliver Josephs, Ralf Deichmann,
John Ashburner, and Robert Turner. "Image distortion correction in
fMRI: a quantitative evaluation." Neuroimage 16, no. 1 (2002):
217-240.
2) Simulated fieldmaps, from segmenting air from tissues in the MRI.
See eg. Poynton, Clare, Mark Jenkinson, Stephen Whalen, Alexandra
Golby, and William Wells. "Fieldmap-free retrospective registration
and distortion correction for epi-based functional imaging." Medical
Image Computing and Computer-Assisted Intervention–MICCAI 2008 (2008):
271-279.
3) Nonlinear registration between EPI and T1w.
Best regards,
-John
On 11 February 2013 18:44, Bianca van den bulk
<[log in to unmask]> wrote:
> Dear SPM-list
>
> We tried some of your suggested and further compared our registered and normalized pictures. However, we're still puzzled on the normalisation to T1/EPI template.
>
> For a reference I attached a ' compare registration' pic: the upper right picture is normalization using 'segmented' procedure, the middle right picture using a 'T1' normalization (they look approximately the same).
>
> Both normalization appear ok, but given the T1 template (lower left picture), (especially..?) the visual cortex seems somewhat 'shrinked'
> However, normalizing epi to epi template (see middle left picture) gives an accurate outer match of the brain.
>
> We reoriented the 0, 0, 0 point in the T1 images to be at the Ant Com. Also realignment between mean-epi and T1 seems fine.
> Any ideas on what the T1 vs EPI normalization difference is caused by?
>
> Suggestions and comments are very much appreciated!
> Bianca
>
>
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