[FieldTrip] leadfields MNI-coordinates

[Stan van Pelt]

Hi Jan-Mathijs,

 

Thanks, this indeed did the trick!

 

Ergo, forward warping of coordinates 'pos' work like this:

-          mri_realign_mni=ft_volumenormalise([],mri_realign)

-
mnipos=ft_warp_apply(mri_realign_mni.params,ft_warp_apply(mri_realign_mni.
initial, pos,'individual2sn')

 

Inverse warping returns coordinates of mnipos in subject space (ctfpos):

-
posback=ft_warp_apply(mri_realign_mni.params,mnipos,'sn2individual')

-          ctfpos= ft_warp_apply(pinv(mri_realign_mni.initial),posback)

 

Best,

Stan

 

From: fieldtrip-bounces at science.ru.nl
[mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of jan-mathijs
schoffelen
Sent: dinsdag 23 september 2014 7:22
To: FieldTrip discussion list
Subject: Re: [FieldTrip] leadfields MNI-coordinates

 

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


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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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