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

[Noam Peled]

Hey Chris,
We've developed the "grids and strips electrode localization utility" tool
in our lab, so please let me know if you have any questions.
For electrodes plotting, we developed a visualization tool in python which
is based on Blender, a free source 3D visualization tool.
You can take a look on a quick demo here (It's better to watch it on a
desktop computer and not on a smartphone, otherwise you won't be able to
see the annotations):
https://www.youtube.com/watch?v=tJzoRWbseKw
The tool is for multi-modality neuroimaging data visualization, like fMRI,
MEG, invasive electrodes, etc. 5 minutes into the demo you can find how to
visualize depth electrodes.
Let me know if you want to use it.

Best,
Noam

On Mon, Nov 23, 2015 at 2:11 PM Chris Holdgraf <choldgraf at berkeley.edu>
wrote:

> 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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