[FieldTrip] Intracranial Data

[Arjen Stolk]

Hi Raghavan,

Let me include the mailing list in this answer, as perhaps others want to
chime in. For instance, I have no experience with extracting monkey
cortical surfaces from MRIs. As for fusing the CT with the MR, all that
matters is that the two anatomical images are aligned to the same
coordinate system. In the protocol, the ACPC coordinate system is chosen
because it is a preferred convention for FreeSurfer, hence, both anatomical
images are aligned to it. Skipping the FreeSurfer-based cortical
extraction, it should be no problem fusing the scans in another coordinate
space, say the CTF coordinate space. The easiest way to achieve this is by
specifying cfg.coordsys = 'ctf' at step 4, instead of 'acpc', and leave out
the automatic conversion of the CT scan to ACPC from CTF (step 12). Make
sure to now localize the CTF landmarks (nasion, left, right ear canals) in
step 4 and not the ACPC landmarks. Finally, you might want to change
cfg.coordsys = 'acpc' into 'ctf' in the actual fusion call (step 13). That
should hopefully get you going and allow you to link the
electrophysiological signal to the monkey's anatomy.

Best regards,
Arjen

On Mon, Mar 11, 2019 at 8:39 AM Raghavan Gopalakrishnan <
gopalar.ccf at gmail.com> wrote:

> Hi Arjen,
>
> I am an avid user of fieldtrip, and trying to recreate the methods you
> published in the nature protocols paper “Integrated analysis of anatomical
> and electrophysiological human intracranial data”. The main challenge is
> while the publication is tuned towards human data, I am working with NHP
> (Monkey) datasets.
>
> The processing of anatomical data is a bit challenging. I understand
> freesurfer is not designed to work with non-human data as well. But, I was
> hoping to skip the cortical extraction step and proceed onto fusing CT and
> MRI information as shown in the paper. Volume realigning of ct data to acpc
> coordinates doesn’t seem to work well.
>
> Do you have any resources or pointers that could help me?
>
>
>
> Thanks,
>
> Raghavan
>
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https://doi.org/10.1371/journal.pcbi.1002202