Hi - these issues about AFNI finding structural images not already in
second-level FEAT directories are independent of the version of FSL.
The caveat to that is that for first-level FEAT analyses, OLD FEAT
directories work already with AFNI whilst new (FSL-3, where the other
structural images are in the "reg" subdirectory) ones need the feat2afni
script to be run in the FEAT dir before running AFNI.
:)
On Mon, 20 Jan 2003, Wei Qiu wrote:
> Hi Steve,
>
> If I plan to installed the new version of FSL(5.0). Does this
> problem can be fixes automatically? Thank, wei
>
>
> On Mon, 20 Jan 2003, Stephen Smith wrote:
>
> > Hi - afaik, wrt loading structural images, AFNI at present just looks for
> > analyze images in the current FEAT directory not containing the string
> > "stat". So I think that, yes, the best workaround currently is to copy any
> > structural images you want AFNI to see into the FEAT directory (or link to
> > them).
> >
> > Thanks, Steve.
> >
> >
> >
> > On Mon, 20 Jan 2003, Andy Goldfine wrote:
> >
> > > I found the AFNI rendering plugin to be a great way to view results of my
> > > FSL process but had a problem with the anatomical underlay when viewing
> > > results from a higher level analysis. The rendering plugin from the higher
> > > level analysis only sees the mask as a possible image for an underlay. My
> > > solution was to change the file highres.hdr which was set as a link to
> > > reg/highres.hdr (which doesn't exist in the higher level cope folder)
> > > to ../../lowerlevel.feat/reg/highres.hdr. Is there an easier way for this
> > > to work? Thanks.
> > >
> >
> > Stephen M. Smith
> > Head of Image Analysis, FMRIB
> >
> > 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
> >
>
Stephen M. Smith
Head of Image Analysis, FMRIB
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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