Hi. FEAT does expect data to look like FMRI, in the sense that although
you can turn off BET and set the Misc->threshold to 0, that "0" is
calculated after ignoring the extreme tails of the intensity histogram,
hance will possibly remove some of your ASL data. The easiest workaround
for you is to increase the values within the brain relative to the
background, or, more easily, just pad round the outside of the image with
strongly negative numbers..
Cheers, Steve.
On Sun, 2 May 2004, Luis Hernandez-Garcia wrote:
> Hello,
>
> Could someone help me figure something out? I'm trying to figure out how the mask.img file is
> generated in FSL. I assume it is used to avoid analyzing all the voxels in the image and save some
> time. It is different fromt he "Pre-trheshold Mask" in the "Post-stats" tab, isn't it? From the looks
> of it, it's taking some lower portion of the histogram and setting those values to zero, while
> keeping the others as one.
>
> Is there an option in the interface to select a different mask or do away with it? ( I haven't been
> able to figure it out in the documentation. I apologize if I missed it) I am inerested in analyzing
> ASL data, which has low SNR or sometimes is negative.
>
> thank you very much,
>
> -L
>
Stephen M. Smith DPhil
Associate Director, FMRIB and Analysis Research Coordinator
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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