[FieldTrip] SPM12 for segmentation and (inverse) normalization
Schoffelen, J.M. (Jan Mathijs)
jan.schoffelen at donders.ru.nl
Thu Sep 21 09:09:06 CEST 2017
Please note that FT now has full support for SPM12, both using the old-style segmentation, and the new one (the latter yielding 6 tissue types).
On 20 Sep 2017, at 17:03, Stephen Whitmarsh <stephen.whitmarsh at gmail.com<mailto:stephen.whitmarsh at gmail.com>> wrote:
I having some problems in normalizing MRIs for my study. Some have improper segmentation for which changing individual brain/scalp thresholds works in many cases but not all, e.g. when the scalp 'bleeds' into some noise outside of the head. Also, changing parameters in spm8 for normalization, such as number of iterations (directly in in spm_normalize, since FT does not pass these parameters) improves the transformation.
However, some scans I cannot deal with, either because they have noise from outsides of the head 'bleed' onto the scalp, thereby preventing optimal scalp-segmentation and thereby normalization. Others have an inappropriate contrast MRI sequence.
Some fMRI researchers advised me to use SPM12, because of its improved preprocessing procedures. However, it does not seem supported in FT yet. Does anyone have experience with this, and can perhaps share how they extracted the transformation matrix from the resulting nifti's?
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