[FieldTrip] SPM12 for segmentation and (inverse) normalization

Stephen Whitmarsh stephen.whitmarsh at gmail.com
Wed Sep 20 17:03:52 CEST 2017

Dear all,

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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