[FieldTrip] SPM12 for segmentation and (inverse) normalization

Stephen Whitmarsh stephen.whitmarsh at gmail.com
Thu Sep 21 14:36:43 CEST 2017

Dear Sarang and Jan-Mathijs,

Thanks a lot. I am now able (after updating FT, which now includes SPM12 in
/external), to use SPM12 for segmentation of my template and my subject
MRI, by using cfg.spmversion = 'spm12'. 12 is definitely is a big
improvement over 8 when it comes to brain-segmentation, which now does not
require individual treatments anymore. It also outputs more compartments
which gives me a little bit more to work with when dealing with scans that
have bad delineation of the scalp for normalization.

Pleas note that defaults seems to differ - some FT functions default to
spm8, others to spm12.

In fact, FT still reverts to spm8 in ft_volumenormalise when called in
ft_prepare_sourcemodel, even when calling the latter with cfg.spmversion =
'spm12'. In other words the cfg.spmversion is not passed along.

Best wishes and thanks again!

On 21 September 2017 at 09:09, Schoffelen, J.M. (Jan Mathijs) <
jan.schoffelen at donders.ru.nl> wrote:

> Hi Stephen,
> 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).
> Best,
> Jan-Mathijs
> On 20 Sep 2017, at 17:03, Stephen Whitmarsh <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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