Hi,
It is really hard to tell what is happening from these jpgs.
Firstly, I would recommend performing the unwarping
via the FEAT GUI (in the prestats). This automatically
cleans up noisy voxels at the edge of the brain and does
other niceties.
You still need to get a correct rad_s fieldmap input though.
Presently, it doesn't look like you have the phase set correctly
as the rangeout_phase_rad_s and ring_phase_rad_s images
look full of wraps. Do these disappear after prelude is run?
That is, are the unwrapped_rad images smooth and without
sharp edges inside the brain? If there are wraps then either
the initial phase is not set correctly, or the unwrapping is failing,
which can happen with poor masking. In general we recommend
running BET on the magnitude image to generate a mask to use
with prelude.
As for the phase scaling, your processing only works if the initial
image ranges from -A to +A, in which case the output ends up
from -pi to +pi. Otherwise, if it is just 0 to +A then the output is
0 to +pi which is not correct (there needs to be a 2*pi range).
With respect to the corrected images, they show some streaks
which should be cleaned up by using a BET mask on the
magnitude image when you pass it into FEAT (or even into
the fugue command line if you prefer).
All the best,
Mark
On 27 Nov 2008, at 14:36, SUBSCRIBE FSL Anonymous wrote:
> Dear all,
>
> We tried to use FSL for fMRI phase map corrections. However, we
> encounter
> some troubles as you can see on the images we posted here:
> http://dl.free.fr/uJwchrtHB/fMRI_Phase_Map.zip.
> Here is the list of the tasks we performed:
>
>> fslstats subject_TE10_phase.nii.gz -R -> get the |max| A of the
>> images
>> fslmaths -dt float subject_TE10_phase.nii.gz -div A.0 -mul 3.1415927
> subject_TE10_phase_div -odt float
>> prelude -a subject_TE10_magnitude.nii.gz -p
>> subject_TE10_phase_div.nii.gz
> -o subject_TE10_phase_unwrapped_rad
>
> Same with TE15
>
>> fslmaths subject_TE15_phase_unwrapped_rad.nii.gz -sub
> subject_TE10_phase_unwrapped_rad.nii.gz -div 0.005 phase_rad_s
>> fugue -i epi.nii.gz --dwell=0.000896 --loadfmap=phase_rad_s.nii.gz -u
> epi_corrected
>
> We would be much grateful if you could explain us what is the
> artefacts on
> the snapshots and how to correct them.
>
> Thanks in advance for your help,
> Best regards,
>
> Alexandre.
>
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