Hi Steve,
The smoothing argument makes sense and this would seemingly be an improvement
over the older version. However, the extreme edges of the mask are supposed to
go beyond actual brain voxels (i.e., the mask is supposed to be
overinclusive),
so blurring these non brain voxels with the background shouldn't really matter
unless the smoothing kernel is huge (I think).
In any case, the end result is a mask that tends to exclude voxels that
I would
like to keep. For example, please see the attached image of a 3rd level mask
that was derived from first level feats that all had a reduced brain/non-brain
threshold of 1%. This is certainly an improvement over using the default
setting (which I posted about back in October), but it isn't perfect,
especially in comparison to the older version of FSL. OFC, parietal cortex and
other areas have holes in them.
As a fix, could I simply run all of the preprocessing steps from the command
line and do the smoothing before BET? I suspect all of the typical options
within the pre-stats tab have easily scriptable programs (the only one I'm not
sure about is the highpass filter).
Thanks,
David
--------------------------------------------------
David V. Smith
Graduate Student, Huettel Lab
Center for Cognitive Neuroscience
Duke University
Durham, NC 27708
www.mind.duke.edu
--------------------------------------------------
Quoting Steve Smith <[log in to unmask]>:
> Hi - yes, this is expected I think, and in general is due to an
> "improvement": in the old version, the spatial smoothing was just
> applied homogeneously across the whole image, including the effect of
> blurring the edges of the brain into the background. In FSL4.0 this
> is improved - the smoothing kernel is limited to lying only within
> the brain mask area, so that non-brain voxels are not included into
> the smoothing of near-brain-edge voxels. I think that this in
> general a better thing to do - one can't argue that the non-brain
> voxels have any useful information to add to the near-brain-edge
> voxels - and explains what you're seeing here. If you really think
> that this is ending up excluding voxels that you want kept in (which
> I suspect it's not), then yes you can just reduce the
> brain/non-brain threshold value if you prefer that.
>
> Hope this makes sense? Cheers, Steve.
>
> p.s., Note that none of the above affects head motion correction or
> registration, both of which effectively happen before spatial
> smoothing.
>
>
>
>
> On 27 Nov 2007, at 05:17, David V. Smith wrote:
>
>>
>> Hi,
>>
>> I've had trouble with the quality of the masks that I'm getting from
>> the new
>> version of FSL; however, the older versions of FSL seem to make
>> masks that are
>> perfectly fine. See attached image.
>>
>> What's changed with the new version of FSL, and how can I make it
>> produce masks
>> like the older version? These differences are not subtle and they
>> led to the
>> significant problems I posted about earlier
>> (http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0710&L=FSL&P=R68794&D=0&H=0&I=-3&O=T&T=0
>> ).
>> I've tested this on data from different scanners and I don't think
>> the problem
>> is because of data quality or "weird intensities" as Steve suggested
>> earlier.
>>
>> Reducing the %Brain/Background setting to 1 has helped a little, but I was
>> hoping you guys could tell me if anything is wrong with the new
>> version and if
>> something is wrong, how can it be fixed.
>>
>> Thanks,
>> David
>> <fsl_mask_comparison.png>
>
>
> ---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> ---------------------------------------------------------------------------
>
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