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

[Chris Holdgraf]

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_
>>>>
>>>
>>>
>>> _______________________________________________
>>> Mne_analysis mailing list
>>> Mne_analysis at nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom
>>> it is
>>> addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail
>>> contains patient information, please contact the Partners Compliance
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>> in error
>>> but does not contain patient information, please contact the sender and
>>> properly
>>> dispose of the e-mail.
>>>
>>>
>>
>>
>> --
>> _____________________________________
>>
>> PhD Candidate in Neuroscience | UC Berkeley <http://hwni.org/>
>> Editor and Web Director | Berkeley Science Review
>> <http://sciencereview.berkeley.edu/>
>> _____________________________________
>> _______________________________________________
>> Mne_analysis mailing list
>> Mne_analysis at nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>


-- 
_____________________________________

PhD Candidate in Neuroscience | UC Berkeley <http://hwni.org/>
Editor and Web Director | Berkeley Science Review
<http://sciencereview.berkeley.edu/>
_____________________________________
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20151124/0e0dbcb3/attachment.html