Hi Torsten,
Yes, I can imagine that this might happen. There isn't a totally easy fix,
but you could change the masking (for everyone on your system) by taking
the file $FSLDIR/tcl/featlib.tcl and changing the line:
fsl:exec "${FSLDIR}/bin/applywarp -i grot$pad -o grot$pad --premat=mc/prefiltered_func_data_mcf.mat/MAT_$pad -w unwarp/EF_UD_warp -r example_func --abs --mask=unwarp/EF_UD_fmap_mag_brain_mask"
TO
fsl:exec "${FSLDIR}/bin/applywarp -i grot$pad -o grot$pad --premat=mc/prefiltered_func_data_mcf.mat/MAT_$pad -w unwarp/EF_UD_warp -r example_func --abs"
AND the line
fsl:exec "${FSLDIR}/bin/applywarp -i $funcdata -o prefiltered_func_data_unwarp -w unwarp/EF_UD_warp -r example_func --abs --mask=unwarp/EF_UD_fmap_mag_brain_mask"
TO
fsl:exec "${FSLDIR}/bin/applywarp -i $funcdata -o prefiltered_func_data_unwarp -w unwarp/EF_UD_warp -r example_func --abs"
This will turn off the masking at this stage. It should then get masked later on in the
same way as images do when the fieldmap correction is not applied. Hopefully that
will fix the problem.
If you don't want to change it for everyone then you can always make a local copy
of FSL, set up your FSLDIR to point to your local copy (if you don't do this in your
setup file - e.g. .bash_profile - then you'll also need to do ". ${FSLDIR}/etc/fslconf/fsl.sh"
after you've set the FSLDIR) and then you can run from your own local copy and
modify it without affecting others.
We will have a different solution to the masking in the next release, but until then
I think this is your best option.
All the best,
Mark
On 20 Jul 2011, at 15:31, Torsten Ruest wrote:
> Hi there,
>
> I noticed that during the preprocessing in feat there is an erosion applied to the fieldmap-magnitude mask which is then propagated onto the fMRI data. It chops of quite a junk from the fMRI data while I think for our data this erosion step takes off just a bit too much - the fieldmap has been quite nicely and neatly been brain extracted. Is there a way to switch this off?
>
> Thank you very much in advance,
>
> Torsten
>
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