Hi,
This behaviour with scl_slope being set incorrectly after fsl programs
run has been noticed before and we have a workaround solution that
we announced in the FSL patches (4 August 2005) - see below.
Essentially, what you need to do is to run the patched version of
avwmaths as a pre-filter. That is, run it on all inputs to FSL where
the scl_slope or scl_inter are not 1.0 and 0.0 respectively (note
that a scl_slope of 0.0 is "corrected" to a value of 1.0 internally).
To see if this is necessary for any particular file, just run avwhd
on the
file and look at these two entries.
All the best,
Mark
>
> Stephen Smith wrote:
>
> We've just released a patch with a couple of new minor features and a
>
> few minor bug fixes for FSL-3.2b:
> 1. fdr (false discovery rate) command-line program "fdr" now added.
>
> 2. mm (mixture modelling) minor changes and bug fixes.
>
> 3. renderhighres GUI and script re-written to give slightly improved
>
> functionality.
>
> 4. flirt minor bug fix (for when you use -init AND wide starting
> search)
>
> 5. avwstats++ minor bug fix when using a mask.
>
> 6. some programs didn't deal right with scaling/intercept values in
>
> the header (which FSL doesn't write, but should read correctly as a
>
> scaling/translation of data values). most programs are not yet fixed
>
> to work right with these values in the header. The workaround: the
>
> patch contains a new version of avwmaths which should be run before
>
> any other FSL programs on such images to create new versions which
>
> have the scaling/intercept "moved" into the data values.
>
> 7. fast (segmentation) had a bug in the 2-class ("-2") option -
>
> sometimes in this case it only ran one iteration, which caused
>
> problems (for example) if there was bias field present.
>
>
>
> To get the patch is easy; EITHER re-download FSL
>
> from scratch, or just take the appropriate small patch file from
>
> http://www.fmrib.ox.ac.uk/fsldownloads/patches/3.2
>
> and then:
>
> cd $FSLDIR/..
>
> gunzip [your downloaded patch file]
>
> tar xvf [the uncompressed patch file]
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