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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