Hi Michael,
Which version of FSL are you using? from 4.1.7 the top-level example_func should be the same as EF_UD_example_func.nii.gz without apply the fieldmap mask. Does this match with what you are seeing?
pre 4.1.7
${FSLDIR}/bin/applywarp -i example_func_orig_distorted -o example_func -w unwarp/EF_UD_warp -r example_func_orig_distorted --abs --mask=unwarp/EF_UD_fmap_mag_brain_mask
post 4.1.7
${FSLDIR}/bin/applywarp -i example_func_orig_distorted -o example_func -w unwarp/EF_UD_warp -r example_func_orig_distorted --abs
> 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]
> --------------------------------------------------------------------
>
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