[Mne_analysis] What do people use for fMRI/MRI processing?

[Chris Holdgraf]

Yep - I'm only talking about structural, not functional. We have a similar
problem in ECoG, but in our case we need to localize electrodes on the
cortical surface. We don't have an MRI of these electrodes, but we do
usually have CT scans. So I'm trying to find a python pipeline for
co-registering the CT (where the electrodes are) to the MR (where the
anatomy is). E.g., I asked on the neuroimaging listserv and someone has put
together a GUI for something like this:

https://github.com/aestrivex/gselu/

The reason I'd like to do this is in order to use Freesurfer for the MR
processing / surface extraction, and then to do electrode plotting on top
of that.

Chris

On Mon, Nov 23, 2015 at 8:48 AM, Denis-Alexander Engemann <
denis.engemann at gmail.com> wrote:

> No ambiguities here, of course you need a structural scan. I might hav
> misread Chirs' question. We commonly use Freesurfer here. But we don't need
> functional scans.
>
> On Mon, Nov 23, 2015 at 5:46 PM, Tom Holroyd <tomh at kurage.nimh.nih.gov>
> wrote:
>
>> > Actually less so, speaking for people I know. You don't need fMRI to
>> > source localize MEG.
>>
>> You generally DO need a structural MRI, for calculation of the inner
>> skull surface used in generating theoretical magnetic fields. Without
>> an MRI you can only approximate the shape of the brain using a sphere.
>> Multisphere or Nolte is typically used given a real brain shape. AFNI's
>> 3dSkullStrip is fine for generating the surfaces.
>>
>> --
>> Dr. Tom
>> --
>> "I am, as I said, inspired by the biological phenomena in which
>> chemical forces are used in repetitious fashion to produce all
>> kinds of weird effects (one of which is the author)."
>>         -- Richard Feynman, _There's Plenty of Room at the Bottom_
>>
>
>
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PhD Candidate in Neuroscience | UC Berkeley <http://hwni.org/>
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