Dear SPM experts,
we have problems normalizing whole brain EPI images using SPM99.
Relating to an earlier mail on the list, we chose the following steps:
after realignment: coregistering of the T1 structural scan to the mean
EPI from realignment
determination of the normalisation parameters for the mean EPI image
(EPI template, bounding box: template, as we are interested in the whole
brain, sinc interpol. voxel size 2x2x2) and applying those parameters to
all functionals and the structurals.
both, functional and structural scans look quite distrored, the size of
the images is greater than the glass brain in both x- and y- direction.
Now, I have read on the mailing list, that the 'mask brain' option might
be responsible for the problem when normalizing EPI images. When turning
off this option in the normalisation defaults, the normalised EPI scans
look much better, however the T1 scans show some additional distortions
(resembling those of the EPI images). The size of those normalized
functionals and structurals is o.k.
Can anybody tell us, what is the best approach to normalize both
functionals and structurals:
- disabling brain masking during normalisation?
- seperately normalizing the T1 scans to the T1 template?
- determination of normalisation parameters for the T1 scans (with brain
masking) and applying them to the functionals?
- is there a problem with applying the template bounding box instead of
the defaults bb?
Thank you very much in advance
Bernhard Haslinger
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Dr. Bernhard Haslinger
Neurologische Klinik
Klinikum Rechts der Isar
TU-München
Möhlstraße 28
D-81675 München
E-mail: [log in to unmask]
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