[FieldTrip] SPM12 for segmentation and (inverse) normalization

[Sarang S. Dalal]

Hi Stephen,

We have a pipeline that can use either SPM8 or SPM12 to perform both segmentation and normalization, though perhaps in a way that’s different from the official FieldTrip tutorials. Have a look at:
https://github.com/meeg-cfin/nemolab/blob/master/basics/nemo_mriproc.m

ft_volumesegment should use whichever SPM is in your path (be careful about fieldtrip/external/spm8!), and (according to my memory) SPM12 sometimes can succeed where SPM8 doesn’t provide good segmentations.

Note that for the normalization in SPM12, our script defines “/OldNorm/T1.nii” as the template, which indeed seems to give results equivalent to SPM8. I think you could change this to SPM12’s default template if you prefer.

NB: we use MRI coordinates as the base coordinate system in our pipelines, so MEG/EEG is transformed to MRI, rather than MRI to MEG/EEG.

Cheers,
Sarang


On 20 Sep 2017, at 17:03, Stephen Whitmarsh <stephen.whitmarsh at GMAIL.COM<mailto:stephen.whitmarsh at GMAIL.COM>> wrote:

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?

Thanks,
Stephen
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