[FieldTrip] Coordsys problems CTF and SPM

Nicholas A. Peatfield nick.peatfield at gmail.com
Sat Sep 24 22:35:36 CEST 2016


Hi Jan-Mathijs,

I found the magical variable T - thanks for the solution!

Regards,

Nick

On 24 September 2016 at 04:27, Schoffelen, J.M. (Jan Mathijs) <
jan.schoffelen at donders.ru.nl> wrote:

> Hi Nick,
>
> You need to use the anatomical MRI that you used to create your headmodel
> etc., register it to ctf-space using ft_volumerealign (in the interactive
> mode, it seems), and then use some magical matrix multiplications to get
> the appropriate transformation matrix that can be applied to the headmodel
> (to get it in ctf space), or (when taking the inverse of this
> transformation matrix) to the grad structure (to get it in spm space).
>
> The solution is embedded here: http://www.fieldtriptoolbox.org/tutorial/
> minimumnormestimate
>
> look for the transform_vox2spm and transform_vox2ctf, and the magical
> variable T.
>
> Best,
> Jan-Mathijs
>
>
> On 24 Sep 2016, at 06:24, Nicholas A. Peatfield <nick.peatfield at gmail.com>
> wrote:
>
> Hi Arjen,
>
> Yeah I looked into that but spm to ctf is not supported. And changing the
> grads to spm seems also not possible. Unless I use ft realignsens but the
> behaviour of that seems a little weird in my experience, and seems more
> suited to electrodes.
>
> Cheers
>
> Nick
>
> On Sep 23, 2016 7:35 PM, "Arjen Stolk" <a.stolk8 at gmail.com> wrote:
>
>> Hi Nick,
>>
>> You may want to have a look at ft_convert_coordsys which can switch
>> volumes between different coordinate systems.
>>
>> Best,
>> Arjen
>>
>> On Sep 23, 2016, at 4:55 PM, Nicholas A. Peatfield <
>> nick.peatfield at gmail.com> wrote:
>>
>> Hi all,
>>
>> I'm getting into a problem wherein I have headmodel that are in SPM space
>> and the grads are in CTF space. I would usually keep all the headmodels in
>> CTF space and align based on that but for this dataset and the format of
>> the MRIs,POS etc... there seems to be some problems (could take longer to
>> explain but lets keep this brief).
>>
>> So this of course leads to the issue that the grad and the headmodel
>> within beamformer_lcmv is misaligned by 90 degrees, which is of course not
>> good. Is there a quick solution that I have not come across to either
>> convert the headmodel to ctf or convert the grad structure to spm coordsys?
>> When I specify in the ft_prepare_sourcemodel I explicitly say (cfg.coordsys
>> = 'ctf') but the outputted sourcemodel is still misaligned between the
>> headmodel and the grads (see attached image - oh and the lf is also
>> misaligned of course).
>>
>> Any help would be greatly appreciated. And I hope that this question
>> hasn't come up before as I did quite a bit of google searching before
>> sending this email.
>>
>> With Regards,
>>
>> Nick
>>
>>
>> <image (3).png>
>> --
>> Nicholas Peatfield, PhD
>>
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-- 
Nicholas Peatfield, PhD
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