Dear Russel,

it’s a problem related to earlier versions not carrying the sform/qform to the --iout. I just reran you data with FSL 5.0.9 and there were no problems.


On 22 Oct 2015, at 23:41, Russell Butler <[log in to unmask]> wrote:


its done. the command was:

topup --imain=imgs.nii.gz --datain=datain.txt --out=output --fout=field --iout=unwarped --config=b02b0.cnf




Le 2015-10-22 07:14, Jesper Andersson a écrit :

Dear Russel,
can you please download all the files you used for your call to topup to and let me know when you have done that? And also please send me the exact command you used to run topup?
best regards Jesper

On 21 Oct 2015, at 22:33, Russell Butler <[log in to unmask]> wrote:

hello, i recently tried to apply topup to correct the EPI distortion in my BOLD images...for some reason however, the unwarped images it outputs are flipped in the y-direction (ie, the front of the brain is now where the back was in the original image, and vice versa), and also, the very bottom z-slice has been moved to the top of the image (this only happens for one slice). oh and also, the warp field it outputs is flipped in the y as well. 

anyone else had this problem in the past? other than that, it seems to correct the distortion. i'm pretty sure my dwell time calculation is correct also.