Hi - I assume you are talking about FEAT analysis and output.
The binary brain mask image "mask.hdr" in the FEAT directory is normally
produced by the filtering program "ip" which is run after BET. So BET will
already have removed a lot of the non-brain parts of the image, and then
ip removes more on the basis of the minimum intensity value for each time
series. Thus to change what masking gets done you could turn off BET and
alter the "Brain/background threshold" in the "Misc" section.
COG means "centre-of-gravity" - ie the centre of the cluster, where each
voxel's position is weighted by the Z-statistic values in the cluster.
Note that for very weird shaped clusters, the COG is not guaranteed to be
part of the cluster!
Thanks, Steve.
On Sat, 30 Nov 2002, Jimmy Jensen wrote:
> Dear FSL,
> I wonder how the individual binary mask is made or defined? Is it possible
> to make it larger? I also wonder what COG means in the output HTML?
>
> Regards
> Jimmy
>
>
> --------------------------------------------
> Jimmy Jensen, PhD
> PET centre
> Centre for Addiction and Mental Health
> Clarke Division
> 250 College St.
> Toronto, ON, M5T 1R8
>
> Phone (416) 535-8501 ext. 6280
> Fax (416) 979-4656
>
Stephen M. Smith
Head of Image Analysis, FMRIB
Oxford University Centre for Functional MRI of the Brain
John Radcliffe 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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