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

[Christopher Bailey]

Hi Chris,

You might find SimNIBS (http://www.simnibs.de) interesting. They put together a nice pipeline using Freesurfer, FSL and others to pull of good BEM-segmentations (see also their documentation for suggestions on MR sequences to run). A major part of their work is then related to tessellation for FEM, which may be relevant, depending on how “deep” you need to go when modelling your ECoG data.

Cheers, Chris
--
Christopher Bailey, MSc
MEG Engineer, MINDLab Core Experimental Facility
Center of Functionally Integrative Neuroscience (CFIN)
Aarhus University, Denmark

On 20 Nov 2015, at 18:59, Chris Holdgraf <choldgraf at berkeley.edu<mailto:choldgraf at berkeley.edu>> wrote:

Good idea - will do. Don't MEG people do lots of MRI stuff? In tandem with source localization etc?

On Fri, Nov 20, 2015 at 9:57 AM, Alexandre Gramfort <alexandre.gramfort at telecom-paristech.fr<mailto:alexandre.gramfort at telecom-paristech.fr>> wrote:
hi Chris,

you should ask this question on the neuroimaging at python.org<mailto:neuroimaging at python.org> mailing
(former nipy list).

anatomical registration is so far out of the scope of MNE but maybe
someone here can help using freesurfer/fsl tools I personally don't
master.

Alex


On Fri, Nov 20, 2015 at 6:10 PM, Chris Holdgraf <choldgraf at berkeley.edu<mailto:choldgraf at berkeley.edu>> wrote:
> Hey all - I'm starting to get a bit into the world of MRI preprocessing for
> an ECoG project. We have a number of tools in the lab that do this in
> Matlab, but I'm wondering if such tools exist in python as well.
>
> For example, a post-doc in our lab is one of the developers of Fieldtrip,
> and he's been using their calls to SPM (or FSL) to do CT-MRI coregistrations
> in Matlab. Does something like this exist in python, or do most people go to
> an external package / use Matlab?
>
> Chris
>
> --
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