Hi Matthew,
not quite. I am seeing the same as Michael, i.e. top-level example_func is
not the same as unwarp/EF_UD_example_func.nii.gz .
How come?
Cheers,
Andreas
PS: I have not yet checked the logs which should be informative.
Am 03.07.12 14:31 schrieb "Matthew Webster" unter
<[log in to unmask]>:
>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]
>> --------------------------------------------------------------------
>>
