Hi there, wonder if someone could help me out
We obtained 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).
Does anyone know why these artifact is observed and how to prevent or correct it?
I appreciate your kind help.
Of course Erik,
the input images consist of a single nii file (AP_PA_b0.nii) containing one volume with phase encoding direction being AP 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 (obtanined 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.
Thank you for your help
Do the AP and PA volumes have exactly the same matrix and readout time?
Have you tried topup without the --subsamp flag?
Which version of FSL are you using?
Jerome
Hello Jerome,
Yes, both volumes have the same matrix size and readout time, it it exactly the same sequence except for the phase encoding direction.
I tried to run topup without subsamp command but it didn't work. I guess that's because we acquired 35 volumes and default is an even number (I think 2 or 4).
I'm using FSL 5.0
Thank you for your answer.
Jonathan Gallego
How many slices in each volume? It must be an even number for topup to work. Number of volumes doesn't matter.
Jerome
hello Jerome,
we obtained 35 slices that why the subsamp param was set in 1 because with an even number it did not work, you think this may be related with the artifacts in the final output of topup?
Yes, possibly. I think the next step is to delete 1 slice from each volume e.g. the top or bottom slice from each volume. If bottom slice is deleted from 1 volume, make sure to delete the bottom slice from all volumes (not 1 slice from 1 volume and 1 slice from another volume etc). Then try topup again without the subsamp param.
Jerome
Hi Jonathan Eliezer Gallego Rudolf, I also tried your same approach and the images looked much better. However, I have one question: We specifically acquired field maps for both AP and PA phase encoding images (these are 2 resting state scans) and was wondering if you have any experience in using topup with the actual field maps and then use applytopup to the functional data. We have a SIEMENS prisma scanner.
Best,
Omar
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