Hi everyone, wonder if someone could help me
I have obtained GRE EPI images in a GE MR scanner with opposite phase encoding direction in order to construct a B0 inhomogeneity fieldmap using the topup command in FSL. The problem is that the fieldmaps obtained show some kind of artifact represented by vertical lines in the phase encoding direction (A-P).
The input images consist of a single nii file (AP_PA_b0.nii) containing GRE EPI images: one volume with phase encoding in the AP direction and one volume with phase encoding in PA direction. I entered the acquisition parameters file indicating the direction of encoding for each volume and the total readout time calculated from the echo spacing time (obtained from the header of the images).
The command I used is:
fsl5.0-topup --imain=AP_PA_b0.nii.gz --datain=acqparams.txt --config=b02b0.cnf --out=my_topup_results --fout=my_field --iout=my_unwarped_images --subsamp=1
It´s the first time I work with fieldmaps, so I just followed the instructions from the FSL topup user guide.
Does anyone know why this artifact is observed and how to prevent or correct it?
Is this related with using GRE EPI images rather than non-diffusion-weighted SE EPI
images?
and if so... is there a way to obtain the fieldmap from GRE EPI images?
Thank you for your help
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