[FieldTrip] Intracranial Data

[Arjen Stolk]

In addendum,

"*Volume realigning of ct data to acpc coordinates doesn’t seem to work
well.*",

you could alternatively guestimate the ACPC landmarks in the CT scan. Thus,
rather than aligning the CT to the CTF coordinate system (in step 11) and
then automatically converting it to ACPC (in step 12), you directly align
it to the ACPC coordinate system by guessing the locations of the anterior
and posterior commissures (in step 11). If that works for you, as evidenced
by a successful fusion in step 13, you could still try to include the
FreeSurfer operation in your routine.


On Mon, Mar 11, 2019 at 9:54 AM Arjen Stolk <a.stolk8 at gmail.com> wrote:

> 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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