Hi Steve,
So, what is the fix that you've implemented? Is
$FeatDir/example_func.nii.gz supposed to be identical to
$FeatDir/unwarp/EF_UD_example_func.nii.gz?
Also, perhaps I'm reading the logs incorrectly, but it appears to me
that Registration does use the "top-level" $FeatDir/example_func.nii.gz
as the input for establishing the affine registration to the highres, so
wouldn't any change to $FeatDir/example_func (if that's what was done in
the patch) have the potential to modify the registration in some
fashion?
thanks,
-MH
On Wed, 2012-06-27 at 13:07 +0100, Stephen Smith wrote:
> Hi - this was not intentional, but none of the processing stages
> depended on that version of example_func in the top-level FEAT output
> (eg the registration did use the corrected example_func) - but yes
> that is something we've already fixed internally - and should be in
> the next patch.
>
>
> Cheers.
>
>
>
> On 25 Jun 2012, at 18:17, Michael Harms wrote:
>
> > Hello,
> >
> > Looking at $FeatDir/example_func.nii.gz in fslview in data processed
> > with field mapping correction, I was trying to figure out why I
> > couldn't
> > find any slices that matched the "Undistorted example_func
> > (example_func)" picture in the Pre-stats report. I subsequently
> > determined that
> >
> > 1) $FeatDir/unwarp/EF_D_example_func.nii.gz and
> > $FeatDir/example_func_orig_distorted.nii.gz are identical
> >
> > 2) But $FeatDir/unwarp/EF_UD_example_func.nii.gz and
> > $FeatDir/example_func.nii.gz are not.
> >
> > Is this intentional?
> >
> > Part of the reason I was looking at this is that when I flipped the
> > "Unwarp direction", I didn't see as a big a difference in the
> > "Summary
> > registration, FMRI to standard space" picture on the Registration
> > report
> > as I would have expected to see frontally, which is due to the fact
> > that
> > example_func (used in the Registration report) and
> > EF_UD_example_func
> > (used in the Pre-stats report) are not the same.
> >
> > Given this, I was wondering if it perhaps might be more informative
> > to
> > construct the Registration summary overlays using EF_UD_example_func
> > when field mapping correction was applied? Or alternatively, apply
> > a
> > mask to example_func so that it matches EF_UD_example_func? (Or
> > would
> > that be a bad thing to do for other reasons?)
> >
> > cheers,
> > -MH
> >
> >
> > --
> > Michael Harms, Ph.D.
> > --------------------------------------------------------------------
> > Conte Center for the Neuroscience of Mental Disorders
> > Washington University School of Medicine
> > Department of Psychiatry, Box 8134
> > Renard Hospital, Room 6604 Tel: 314-747-6173
> > 660 South Euclid Ave. Fax: 314-747-2182
> > St. Louis, MO 63110 Email: [log in to unmask]
> > --------------------------------------------------------------------
> >
> >
>
>
> ---------------------------------------------------------------------------
> 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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