[Mne_analysis] BEM construction - FLAIR vs FLASH?

dgw dgwakeman at gmail.com
Fri Feb 28 09:35:30 EST 2014
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Given the contrast in FLAIR  images IMO it would not be possible to
use the standard mne_flash_bem script tools to generate useful bem
surfaces (you could obviously write your own). I can help you out by
saying that in my experience, you can get away with only utilizing the
FLASH 5 data (although this assumes you have similar image quality).
If you are getting very good contrast between the critical tissues, in
your FLASH 5 alone. This should save you half the time.


On Fri, Feb 28, 2014 at 7:36 AM, Alexandre Gramfort
<alexandre.gramfort at telecom-paristech.fr> wrote:
> hi Jon,
>> For BEM construction, can MNE take advantage of Freesurfer's multispectral
>> imaging pipeline (using a single FLAIR scan), or is it still better to
>> collect the two FLASH scans?  I grepped through the linux & python scripts
>> but didn't see anything promising. Cutting a scan would free up some MRI
>> time on a new project, but I don't want to hamstring myself.
> I am not aware of a solution using FLAIR. I guess it could work should you
> dig deep enough in the mne_flash_bem shell script.
> Let us know if you find a way. That would be a nice contribution for MNE users.
> Best,
> Alex
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