[FieldTrip] SPM12 for segmentation and (inverse) normalization
Stephen Whitmarsh
stephen.whitmarsh at gmail.com
Thu Sep 21 18:20:47 CEST 2017
Hi Arjen,
Thanks, and good to hear you've not been let down yet. It might be the fact
that I have some bad quality MRIs to deal with. However... does this
problem (see attached) ring a bell for anyone?:
Brain segmentation is proper, and co-registration with polhemus head-shape
as well, but inverse warp to MNI result in a tilted grid. Linear vs.
non-linear transformation gives the same result. Other subjects going
through the same procedure work fine, except two others wherein I
identified it as a problem in segmenting the scalp and therefor the first
step of the normalization. This one looks absolutely fine in every other
regard, however.
I'm stumped...
cfg = [];
cfg.spmversion = 'spm12';
cfg.grid.warpmni = 'yes';
cfg.grid.template = template_grid;
cfg.grid.nonlinear = 'yes';
cfg.mri = mri_realigned;
cfg.grid.unit = 'mm';
subject_grid = ft_prepare_sourcemodel(cfg);
Cheers,
Stephen
On 21 September 2017 at 17:00, Arjen Stolk <a.stolk8 at gmail.com> wrote:
> Hey Stephen,
>
> Look for discussions regarding spm12 and also dartel on bugzilla. It's
> been a while but as far as I can remember ft_volumenormalize is the only
> function now that has not been integrated. Reason being that it wasnt
> straightforward to house the dartel procedure under a single function, so
> this is ongoing work still. You can however use spm12's coregistration
> function with ft_volumerealign (for rigid body transformations), which Im
> using quite a bit and never let me down (and is much faster than before).
> But that wouldnt work for normalization to template space though (use spm8).
>
> Best
>
> On Sep 21, 2017, at 6:56 AM, Herbert J Gould (hgould) <hgould at memphis.edu>
> wrote:
>
> I have retired please remove me from the mail list
>
> Herbert Jay Gould
> Professor Emeritus
> The University of Memphis
>
>
>
> Sent from my Verizon Wireless 4G LTE smartphone
>
>
> -------- Original message --------
> From: Stephen Whitmarsh
> Date:09/21/2017 7:43 AM (GMT-06:00)
> To: FieldTrip discussion list
> Subject: Re: [FieldTrip] SPM12 for segmentation and (inverse)
> normalization
>
> 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!
> Stephen
>
>
>
> 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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>>
>>
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