[FieldTrip] leadfields MNI-coordinates

[Stan van Pelt]

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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