Hi - yes FIX expects to have to regenerate the WM segmentation - however there is a workaround for the HCP pipeline - where, if you name files correctly it won't get rerun - have a look at the pre-setup stuff in hcp_fix and fix_0b_apply_fast to see this - but this is all undocumented stuff so you'll need to work that out for yourself I"m afraid ;-)
Cheers.
> On 8 Dec 2014, at 11:49, Sean Froudist-Walsh <[log in to unmask]> wrote:
>
> Dear FSL experts and users,
>
> I am running FIX to clean up some of my fMRI data, and I have already run BBR to coregister the functional to the structural data and FNIRT to get to the standard space. I hoped that FIX would be able to use the white matter boundary etc from BBR, but apparently it is not doing that as I get the following messages when I run it:
>
> create edge masks
> run FAST
> registration of standard space masks
> extract features
>
> Do I need to move or rename my reg folder or is it really necessary to run FAST again?
>
> My command is
>
> fix -c ${j}_abstract_art.feat mycustom_training.RData 20
>
> It would save some vital time if these steps didn't have to be run. All comments are much appreciated.
>
> Many thanks,
>
> Sean
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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR 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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