Hi,
This is covered in the FSL course lecture on registration.
The relevant slide text is:
Mask values are normally 0 and 1 (integer format)
- Interpolation gives values in between
- if truncated to integer ==> mask "shrinks”
- Need to re-threshold (binarize) the transformed mask
- "Correct" thresholding depends on the particular case
- Threshold near 0.0 to include partial-volume edges
- Threshold near 1.0 to exclude partial-volume edges
- Threshold at 0.5 to keep the same size (approx)
So the answer depends on your application, and whether
you want to be conservative, inclusive or keep the
mask about the same size (in mm^3).
All the best,
Mark
On 9 Jan 2011, at 08:23, Susan wrote:
> Hello,
>
> I have converted a binary structural ROI (created from the Harvard Oxford atlas) into individual functional space for use in a PPI analysis. The resulting mask (when viewed in FSLview) is no longer binary.
>
> To convert the mask, this is what I did:
>
> flirt -in STGmask -ref example_func -applyxfm -init reg/standard2example_func.mat -out S102_STGmask
>
> Based on searching the forum, my best guess is that I need to apply a threshold to this new mask using some combination of -thr and -bin... but I'm not quite sure how to go about choosing the appropriate -thr value. Any help would be greatly appreciate!
>
> Susan.
>
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