[Mne_analysis] Strictly Positive Source Space Estimates

[Rockhill, Alexander P.]

Hi Hari,

    All the inverse parameters of make_inverse_operator are their defaults, i.e. loose = 'auto' and fixed = 'auto'. The source space was set up using the command "mne_setup_source_space --ico -6 --cps --overwrite". From the documentation, I am interpreting that this would cause the loose value to be 0.2 and therefore the constraint on the orientation is 80% fixed. The source space data is of the kind (number of sources x number of time points) so I am not sure how the three orientation components could be encoded without another dimension i.e. (sources x time points x direction).

     I thought the red in the source space plot corresponded to negative values but I may be interpreting that wrong.

Thanks for the help,

Alex

________________________________________
From: mne_analysis-bounces at nmr.mgh.harvard.edu [mne_analysis-bounces at nmr.mgh.harvard.edu] on behalf of Bharadwaj, Hari M [hbharadw at purdue.edu]
Sent: Thursday, June 07, 2018 1:03 PM
To: Discussion and support forum for the users of MNE Software
Subject: Re: [Mne_analysis] Strictly Positive Source Space Estimates

        External Email - Use Caution

Hi Alex,

Even your stc.plot figure looks like there are only positive values. Do you have a free orientation inverse? It could be that your STC was created to have the vector magnitude, i.e., sqrt(qx^2 + qy^2 + qz^2) of the 3 orientation components.

HTH,
Hari



________________________________________
From: mne_analysis-bounces at nmr.mgh.harvard.edu <mne_analysis-bounces at nmr.mgh.harvard.edu> on behalf of Rockhill, Alexander P. <AROCKHILL at mgh.harvard.edu>
Sent: Thursday, June 7, 2018 12:28 PM
To: mne_analysis at nmr.mgh.harvard.edu
Subject: [Mne_analysis] Strictly Positive Source Space Estimates

Hello,

     When applying an inverse with the dSPM method, it looks like the stc.data is all strictly positive. I am working with a comparison to FieldTrip source space data which is positive and negative. Additionally, when I plot the stc (stc.plot) it looks like there are positive and negative values mapped on to the surface of the brain. Any help on how to get these non-absolute values that show up in the plot would be appreciated.

Thanks,

Alex

Translational NeuroEngineering Laboratory
Division of Neurotherapeutics, Department of Psychiatry
Massachusetts General Hospital, Martinos Center
149 13th St Charlestown #2301, Boston, MA 02129


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