Hi Antonio,
> I notice after running easythresh that there are some voxels showing outside of what
> I defined as the <brain_mask> in easythresh's command line.
> I looked in the script and noticed that there doesn't seem to be any masking being
> done there. I assume that <brain_mask> is not used to actually mask the results, but
> as input for /bin/smoothest. Is this correct?
You are correct, yes. If you want to make sure to get rid of activation
ourside of the mask just change the avwcpgeom and cluster lines (in
fsl/bin/easythresh) to:
${FSLDIR}/bin/avwmaths $1 -mas $2 thresh_$6
${FSLDIR}/bin/avwcpgeom $5 thresh_$6
${FSLDIR}/bin/cluster -i thresh_$6 -t $3 -p $4 --volume=$VOLUME -d $DLH -o cluster_mask_$6 --othresh=thresh_$6 $7 > cluster_$6.txt
BTW - tip of the day - easythresh doesn't give exactly the same answers as
running cluster-based thresholding from FEAT because it estimates data
smoothness from the Zstat image and not the model-fitting residuals
(though in practice it is very similar).
> Also, I was wondering if this similar to the "Pre-threshold masking" option in FEAT.
well - yes and no - that option in FEAT just allows you to specify any old
mask to use at that stage (before thresholding) rather than the one
derived from valid brain data by the first stages of the FEAT run.
> I am using avg152T1_brain for the underlay. Is avg152T1_brain_mask OK as a <
> brain_mask> for easythresh?
yes, though it would be slightly better to use one derived from the data
(eg the mask image in the FEAT directory).
Thanks, Steve.
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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