[Mne_analysis] mne_analyze surface viewer error

Wed Feb 13 13:10:35 EST 2013

Dear Matti,

I alsoe head a few cases with quite distorted skulls so played a bit with the gcaatlas option.
Could it be that the watershed routine expects a particular version of the atlas:

...

Mode:          Atlas analysis
Mode:          T1 normalized volume
Mode:          Use the information of atlas (default parms, --help for details)
GCAread: could not open GCA /localdata/freesurfer/average/RB_all_withskull_2007-08-08.gca for reading
No such file or directory
...

It seems I've got to link the exisiting RB_all_withskull_2008-03-26.gca agains the expected name.
Or it should also be possible to simply pass the gcaatlas name to --atlas on invoking mne_watershed_bem, right?

Thanks and best,
Denis

On Tue, Feb 5, 2013 at 1:54 PM, Matti Hamalainen <msh at nmr.mgh.harvard.edu<mailto:msh at nmr.mgh.harvard.edu>> wrote:

Hello,

The BEM surface segmentation using mne_watershed_bem has gone wrong. There is most probably a way the avoid this. There are new options --gcatlas and --preflood <number> for mne_watershed_bem in the nightly build.
I do not recall which one of them helps, I hope someone at the Martinos can help you.

- Matti

On Feb 4, 2013, at 7:55 PM, Vincent Rupp wrote:

Hello,

I am using mne_analyze to align MEG/MRI coordinates in accordance with the instructions at http://www.martinos.org/mne/manual/sampledata.html#chdijbig. However I am having an issue with some of the way my inflated surfaces appear when displayed in the viewer. I've attached two examples of some particularly bad ones, and the third attachment is an example of what the inflated surface looks like ordinarily. This third image is the same surface as the first one that looks like a block. At what point in processing is my workflow going wrong? Thanks in advance.

Best wishes,

Vincent Rupp
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Matti Hamalainen, Ph.D.
Athinoula A. Martinos Center for Biomedical Imaging
Massachusetts General Hospital

msh at nmr.mgh.harvard.edu<mailto:msh at nmr.mgh.harvard.edu>
mhamalainen at partners.org<mailto:mhamalainen at partners.org>

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