Hello FSL and FS pros,
I am trying to pre process DW images but am not sure how to unwarp images.
We are using Siemens Skyra 3T and output fieldmaps;
2 files output from the scanner;
the first file contains two magnitude files in one
the second file contains the single phase difference image
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FSL
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through FSL we have run
eddy correct, bet the magnitude file, and run fsl prepare fieldmap
(example code below)
I am not sure how to use the prelude and FUGUE command and am unclear on their inputs/outputs
Does anyone in FSL land have a clear tutorial of how to utilize these tools?
for example, given my type of fieldmaps do i need to use prelude?
later through FSL stream we would like to complete
bet preprocessed DW images, dtifit, bedpostx
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FREESURFERS
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I have read over the TRACULA requirements and how to edit the configuration files.
There is mention of eddy current correction that is available through tracula but nothing mentioned for dealing with the warping issue.
Does anyone in freesurfer land have any suggestions on how to tackle this as a part of the tracula data stream?
Any input will be appreciated,
Thanks so much
Joseph Veliz
Brentwood Biomedical Research
VA Hospital West Los Angeles
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example
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#Eddy correction
eddy_correct ${name}_dti.nii.gz /Users/seahorse/Studies/NN/DTI/${name}/${name}DTI_eddy.nii.gz 0
#BET fieldmap mag super tight; exclude all non brain voxels
bet 10001_dtiFMmag1mag2.nii.gz /Users/seahorse/Studies/NN/DTI/10001/10001dtimags_brain.nii.gz -F -m -f 0.85
#generate fieldmap in rad/s for FEAT or FUGUE
fsl_prepare_fieldmap SIEMENS 10001_dtiFMphase.nii.gz 10001dtimags_brain.nii.gz fmap_rads 2.46
#Prelude
prelude -c data --unwrap=result
prelude --complex=data -u result
#FUGUE Utility for Geometrically Unwarping EPIs; performs unwarping of an EPI image based on fieldmap data
fugue -i epi -p unwrappedphase --dwell=dwelltime --asym=asymtime -s 0.5 -u result
fugue -i epi --dwell=dwelltime --loadfmap=fieldmap -u result
