[FieldTrip] leadfields MNI-coordinates

[jan-mathijs schoffelen]

Hi Stan,

Part of the solution you’re looking for probably lies in the fact that both the forward and inverse warp are non-linear transformations (when the volumetric normalization is done with cfg.nonlinear = ‘yes’). In other words, the inverse warp cannot be achieved by a simple linear transformation (i.e. the (p)inv of a xxx.transform matrix). Fortunately, ft_warp_apply supports both ft_warp_apply(params, pos, ‘individual2sn’), and ft_warp_apply(params, pos, ‘sn2individual’). The latter aims to achieve the inverse warp you’re looking for. Probably you need to then also still apply the inverse of mri_realign_mni.initial.

Best,
JM


On Sep 22, 2014, at 5:12 PM, Stan van Pelt <s.vanpelt at psych.ru.nl> wrote:

> Hi Eelke,
> 
> Thanks a lot, I seem to have missed that thread, very informative!
> However, I seem not able yet to do the inverse warping, from MNI-coordinates 
> to CTF-coordinates.
> 
> - First I do
> mri_realign_mni=ft_volumenormalise([],mri_realign)
> 
> - This gives me the transformation/normalization parameters from ctf->mni
> - As an example, I apply them to a random coordinate, here [3 5 6]:
> mnipos=ft_warp_apply(mri_realign_mni.params,ft_warp_apply(mri_realign_mni.initial,[3 
> 5 6]),'individual2sn')
> 
> - This gives me mni-coordinates -6.0652  -21.7174  -57.2273
> - But how can I do the reverse?
> - If I do
> round(ft_warp_apply(pinv(mri_realign_mni.transform),mnipos))
>  I don't get [3 5 6]
> 
> - It seems to me I should do something like
> ctfpos=ft_warp_apply(pinv(mri_realign_mni.params, 
> mnipos),mnipos,'individual2sn')
>  or so, but I am not getting it right...
> 
> Best,
> Stan
> 
> 
> -----Original Message-----
> From: fieldtrip-bounces at science.ru.nl 
> [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Eelke Spaak
> Sent: maandag 22 september 2014 13:20
> To: FieldTrip discussion list
> Subject: Re: [FieldTrip] leadfields MNI-coordinates
> 
> Hi Stan,
> 
> Have a look at this recent thread on the list (4 messages, Tom and me, this 
> is the starting message):
> http://mailman.science.ru.nl/pipermail/fieldtrip/2014-August/008362.html
> I think that might help you.
> 
> Groetjes,
> Eelke
> 
> On 22 September 2014 12:44, Stan van Pelt <s.vanpelt at psych.ru.nl> wrote:
>> Dear FieldTrippers,
>> 
>> 
>> 
>> For sourceconstruction (CTF275 MEG data) at specific ROIs, I want to
>> compute leadfields at specific (MNI-)coordinates in the brain. I am
>> trying to find out how that is most easily done using FieldTrip
>> 
>> 
>> 
>> - The most intuitive way seems to me to warp the MNI template to the
>> individual’s brain
>> (http://fieldtrip.fcdonders.nl/example/create_single-subject_grids_in_
>> individual_head_space_that_are_all_aligned_in_mni_space)
>> , and then apply the warping parameters to the ROI’s MNI-coordinates,
>> and enter the subsequent CTF-coordinates into ft_prepare_leadfield.
>> However, I am not sure where exactly I can find these parameters, and
>> how to apply them. Are these the ones in [gridsrc].params (output 
>> ft_sourcemodel)?
>> 
>> - Alternatively, should I run ft_volumenormalise to warp the brain to
>> MNI-space, and then inversely apply the warping parameters to the
>> ROI’s MNI-coordinates? Again, where can I find the warping parameters
>> in this case, and how should they be applied?
>> 
>> 
>> 
>> Best,
>> 
>> Stan
>> 
>> 
>> 
>> -
>> Stan van Pelt, PhD
>> Donders Institute for Brain, Cognition and Behaviour Centre for
>> Cognition Montessorilaan 3, B.01.34
>> 6525 HR Nijmegen, the Netherlands
>> tel: +31 24 3616288
>> 
>> 
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
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Jan-Mathijs Schoffelen, MD PhD 

Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands

Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands

J.Schoffelen at donders.ru.nl
Telephone: +31-24-3614793

http://www.hettaligebrein.nl

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