Hi Mark,
Yeah, after seeing that the necessary variance already exists in the
'sigmasquareds' file, I realized that the mask would be the hardest
part.
What do you think about defining a single GM mask in standard space, and
then propagating that back to the native space for the calculation? Not
as precise as your suggested approach, but do you think it would really
matter that much? Friedman and Glover used a single GM mask defined in
standard space when they implemented this in their paper.
thanks for your thoughts,
-MH
On Mon, 2011-01-31 at 21:12 +0000, Mark Jenkinson wrote:
> Hi Michael,
>
> This is pretty easy to do.
> The hardest part is getting the mask right.
> Once you do have the mask, all you need to do
> is go to the FEAT directory and run:
> fslmaths mean_func -mul mean_func -div stats/sigmasquareds -sqrt SFNR_image
> fslstats SFNR_image -k GM_mask -P 50
> which will give you the median value within the mask.
>
> So now to the tougher bit - getting the mask.
> I would start by generating a segmentation of the
> T1 structural image. After this, apply the registration
> warps (ideally using a fieldmap-derived warp, but if
> not a 6/7 DOF registration will do) to get the GM
> segmentation back into the space of the functional
> images. Then I would run BET on the functional image,
> multiply the BET mask by the transformed GM mask
> and then threshold the resulting image around 0.9
> and binarise this. The resulting binary image should be
> a reasonable description of a GM mask, and given that
> we will take the median of the voxelwise results, the final
> result will be fairly insensitive to small errors in this mask.
>
> I hope this helps.
>
> All the best,
> Mark
>
>
>
>
> On 27 Jan 2011, at 20:52, Michael Harms wrote:
>
> > Hello,
> > I'm wondering if anyone using FSL has implemented the calculation of an
> > SFNR (signal-to-fluctuation-noise ratio) for each 1st level run using a
> > gray matter mask for task-based fMRI data -- i.e., "SFNR-Type-3-GM-SM-
> > Resid" in the terminology of Friedman and Glover (NI, 2006, 33:471-481).
> >
> > I believe that all the pieces are available in FSL to compute something
> > substantially similar. I'm just wondering if someone has already worked
> > out the details and has a script available that they would be willing to
> > share...?
> >
> > thanks,
> > -MH
> >
> > --
> > Michael Harms, Ph.D.
> > --------------------------------------------------------------------
> > Conte Center for the Neuroscience of Mental Disorders
> > Washington University School of Medicine
> > Department of Psychiatry, Box 8134
> > Renard Hospital, Room 6604 Tel: 314-747-6173
> > 660 South Euclid Ave. Fax: 314-747-2182
> > St. Louis, MO 63110 Email: [log in to unmask]
> > --------------------------------------------------------------------
> >
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