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

[Noam Peled]

Hey Chris,
Sure, any help with the documentation will be a blessing :)

On Tue, Nov 24, 2015 at 12:17 PM Chris Holdgraf <choldgraf at berkeley.edu>
wrote:

> Hey Noam - it looks like a really cool tool. I've been chatting with Roan
> on the repository w/ some issues I had doing the basic co-registration, and
> I'm going to keep working through it to try and make it work. Maybe I can
> help out with sharing my experience for documentation purposes etc. It
> would be great if something like this existed for python, as all of our lab
> uses some combination of SPM/FSL/custom code for this.
>
> Chris
>
> On Tue, Nov 24, 2015 at 9:39 AM, Noam Peled <peled.noam at gmail.com> wrote:
>
>> 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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>
>
> --
> _____________________________________
>
> PhD Candidate in Neuroscience | UC Berkeley <http://hwni.org/>
> Editor and Web Director | Berkeley Science Review
> <http://sciencereview.berkeley.edu/>
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