[Mne_analysis] mne_analyze question

[dgw]

Hi Franklin,

Please keep the list cced so everyone can follow. Well, the MNE matlab
toolbox included can read in the STCs. From there you should be able
to run an ICA on that data fairly easily. I'm not familiar with either
GIFT or GICA, so it will be hard for me to point you in the right
direction there (though if anyone here has a suggestion please chip
in). Otherwise, you can describe to their mailing list the data that
you have (i.e. a matrix in matlab of sources x time (with the sources
being located on a cortical surface)) and see if they can help with
the next step.

HTH,
D

On Fri, Mar 14, 2014 at 3:06 PM, Franklin Lovell Orndorff-Plunkett
<forndor at unm.edu> wrote:
> Hello D,
> I am fairly new to this so my description is still low level.  With the dspm surface we're doing ICA on individuals normal and schizophrenic patients.  Then the hope is to take each of these sets of ICs and average across subjects (maybe GICA is better suited, it's still unclear) then export those ICs to matlab format.  The final analysis is a discrete wavelet transform of those (group or averaged) ICs and then statistical characterization in wavelet space to differentiate between the hallucinating and normal signaling.  We're using the MIALab software for the ICA portion (GIFT/GICA) and they require a nifti format.
> Thank you!
> Franklin
>
> ________________________________________
> From: dgw <dgwakeman at gmail.com>
> Sent: Friday, March 14, 2014 12:53 PM
> To: Franklin Lovell Orndorff-Plunkett
> Cc: mne_analysis at nmr.mgh.harvard.edu
> Subject: Re: [Mne_analysis] mne_analyze question
>
> The dspm source reconstruction is 4 dimensional data on a surface.
> While technically there is some support for this in the mgz format it
> is not well optimized for MEG source reconstructions, and it is
> therefore not supported to convert (so far as I know). Additionally
> there is no support for surfaces in nifti (though there is the gifti
> format, but I don't know if giftis can support time data in them). We
> can probably help you much better if you tell us what you want to do
> with the source reconstructions. All of the MNE formats (stc is
> probably what you are talking about here) are fully readable by both
> MATLAB and python, so we should be able to help you take the next step
> with your analysis.
>
> HTH
> D
>
> On Fri, Mar 14, 2014 at 2:35 PM, Franklin Lovell Orndorff-Plunkett
> <forndor at unm.edu> wrote:
>> MNE Experts,
>> Our group is working with some old MEG data from 2012.  Just started a week
>> or so ago with MNE software and I'm having issues exporting the dSPM source
>> reconstruction to an .mgz (or .nii) file.  Also, after that has been solved,
>> if one can only export the dSPM data to an .mgz/mgh file, is there a command
>> for converting to .nii format? Very new to this, I appreciate your help.
>> Thank you,
>> Franklin
>>
>> _______________________________________________
>> 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.
>>