[FieldTrip] Nonlinear normalization/MNI grid distortions

[Maité Crespo García]

Dear community,
I performed nonlinear normalizations and plotted theresulting MRIs. I noticed the normalized MRIs had unwanted distortions, and wereclearly different from the normalized MRIs obtained directly in SPM. 

I noticed the default parameters (flags) in Fieldtrip’s spm_normalise()are different from SPM’s spm_normalise(). In Fieldtrip, the amount of regularizationis too low (= 0.1, line 144 in spm_normalise) compared with SPM’sdefault (=1). 

This may be a problem not only for normalization but whencomputing MNI-aligned individual grids following the tutorial (“CreateMNI-aligned grids in individual”) because there is an implicit normalizationstep.
Possible solutions: 

-         Call/substitute Fieldtrip’s spm_normalise() bySPM’s function or change Fieldtrip’s default flags values.-         Perform the normalization outside in SPM andprovide the cfg.spmparams.flags. However, there is a bug in ft_volumenormalise()using that option. I think it may be because the flags are not passed to spm_normalise(line 239). As a fix, I have modified the function with the lines below. Butsurely there is a more direct way to avoid the problem.VF        =spm_vol([cfg.intermediatename,'_anatomy.img']);params    =spm_normalise(VG,VF,[],[],[],cfg.spmparams.flags); I wish this report helps.  Best regards,Maité
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20151014/b460a6a0/attachment.html>