[Mne_analysis] BEM construction - FLAIR vs FLASH?

[Christopher Bailey]

Dear Dan, Jon and Alex,

Having recently received the sequence parameters from Alex (thx!) for the multi-echo FLASH, I can second Dan's observation of practically identical surfaces using 5 deg alone vs. 5 and 30 degs. This is on a 3T Skyra, anyone care to weigh in with experiences from other scanners?

My naive take on FLAIR is that it might help getting the pia-dura separation right, i.e., improve cortex thickness estimates, but probably not that critical for M/EEG forward models?

/Chris
/CFIN, Aarhus, Denmark

On Feb 28, 2014, at 3:35 PM, dgw <dgwakeman at gmail.com> wrote:

> 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.
> 
> D
> 
> 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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