Can you provide details of your calls to topup?

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