I'm trying to perform topup on EPI BOLD data.
below are my commands for topup and applytopup.

topup --imain=all_b0s --datain=parameters.txt --config=b02b0.cnf
--out=my_topup_results --fout=my_field --iout=my_dewarped_images
applytopup --imain=bold.nii --inindex=1 --topup=my_topup_results
--datain=parameters.txt --method=jac --interp=spline --out=bold_dewarp

and my parameters.txt file is
0 1 0 1
0 -1 0 1

attached are my B0s, topup field image and BOLD images.
the EPI BOLD image after applytopup looks too much shrunken up in frontal area, and
the field image is very bright in this frontal area.
I don't know this is right thing, but this dewarped BOLD image is mis-registered to
T1 structural image. 

is there anyone have tried topup with BOLD?
thanks,

We have used topup for unwarping of BOLD images as part of the HCP project, and that has worked well for us.

Your command line looks good so I am not sure what is going on here. Your "fieldmap" output from topup looks quite strange to me and those "streaks" in the PE direction are not what you would typically see. Can I ask you to upload all files referred to on your command lines to

and send me an email to notify me when you have done that? Please also tar the files first so that I only need to download a single file.

Jesper

 

Jieun Kim
<B0_images_sm.jpg><field_image_sm.jpg><BOLD_images_sm.jpg>