[Mne_analysis] "Intensity too high" when using mne_watershed_bem

[dgw]

In that case, you may be better off (obviously throwing them out may 
apply, but given you don't want to do that) using an individual who best 
fits the digitized points. The average surfaces have very different 
shape from individual surfaces and do not necessarily make sense to use 
for source reconstruction i.e. the orientations in an average brain will 
be very different from those in the individuals who compose it.

D

Stephen Politzer-Ahles wrote:
> Hi Dan,
> 
> Thanks a lot for your reply. I will send a message to the FreeSurfer 
> list to see what they say.
> 
> Regarding your second question, I have two subjects without MRIs (one 
> was unable to be scanned, and the other one moved during the scan) and 
> was hoping to just analyze their data on an average brain rather than 
> throw them out entirely.
> 
> Best,
> Steve
> 
> On Thu, May 3, 2012 at 11:08 PM, Dan G Wakeman <dgwakeman at gmail.com 
> <mailto:dgwakeman at gmail.com>> wrote:
> 
>     See reply in text
>     On 2012 May 3, at 23:08 , Stephen Politzer-Ahles wrote:
> 
>      > Hello,
>      >
>      > mne_watershed_bem is exiting with the following error:
>      >
>      > w=White Matter =Intensity too high (>240)...valid input ?
> 
>     This error is due to the MRI data having unusually large values. It
>     actually comes from FreeSurfer's mri_watershed program (called by
>     mne_watershed_bem).  You would need to ask the FreeSurfer people
>     about how the volumes are generated by the make average subject and
>     any recommendations about using mri_watershed with them.
> 
>     The analysis you describe does beg another question: Why do you want
>     to generate a BEM for the average subject?
> 
>     D
>      >
>      > I'm running mne_watershed_bem on an average brain I created from
>     23 other
>      > participants using Freesurfer's make_average_subject. I've been
>     able to do
>      > mne_watershed_bem without error on all the other subjects, but I
>     get this
>      > error when using the average breain. Does anyone have any guesses
>     what
>      > could be causing the error?
>      >
>      > Thank you,
>      > Steve Politzer-Ahles
>      >
>      > --
>      > Stephen Politzer-Ahles
>      > University of Kansas
>      > Linguistics Department
>      > http://www.linguistics.ku.edu/
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> 
> -- 
> Stephen Politzer-Ahles
> University of Kansas
> Linguistics Department
> http://www.linguistics.ku.edu/