Hello FSL experts,
I am having trouble using FUGUE in the command line to correct my EPI images before inputting them into a graph theory toolbox. Here are the steps I am following, according to the FUGUE help page.
I download and convert my SIEMENS dicom fieldmaps into the phase and magnitude images. I have two volumes in my magnitude image, so I chose the "best" one, and deleted the other volume. I then skull stripped this magnitude image and used fsl_prepare_fieldmap to ensure my phase image is in rads/s according to the following usage:
fsl_prepare_fieldmap SIEMENS BAM004_pilot_FM_phase.nii.gz BAM004_pilot_FM_mag_brain.nii.gz BAM004_pilot_FM_rads.nii.gz 2.46
I then used the rads output to conduct FUGUE in the command line according to the following usage:
fugue -i BAM004_pilot_Rest_new.nii.gz -p BAM004_pilot_FM_rads.nii.gz --dwell=0.839 --asym=2.46 -u BAM004_unwrapped.nii.gz
My echo spacing is 838.7 ms and my echo time difference is 2.46 ms. I receive the following error when running this sequence:
Unwrappedphasemaps must contain at least two volumes!
Error detected: try -h for help
My phase image from the scanner only contains one volume. Please advise how I can correct this error. Also, please clarify what the usage for --asym is. In the FUGUE help listed in the terminal, --asym is defined as the "spin echo time (sec)", but on the FUGUE wiki help page, --asym is the "echo time difference". Please confirm which --asym is the correct usage and whether it should be in ms or sec.
Thank you for your time,
Alisha
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