[FieldTrip] Coordsys problems CTF and SPM

[Schoffelen, J.M. (Jan Mathijs)]

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<mailto: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<mailto: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<mailto: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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