incorrect option name in function topup

[JPolzehl]

1. function topup is currently (version 2.20.3) not in NAMESPACE
2. fslr:::topup("file.nii", "param.txt", out="outfile")

creates call ( non existent option infile )

topup --infile=file.nii --datain=param.txt --out=out --warpres=10 --subsamp=1 --fwhm=8 --miter=5 --ssqlambda=1 --regmod=bending_energy --estmov=1 --minmet=0 --splineorder=3 --numprec=double --interp=spline --scale=0 --regrid=0 --verbose

instead of ( correct option imain )

topup --imain=file.nii --datain=param.txt --out=out --warpres=10 --subsamp=1 --fwhm=8 --miter=5 --ssqlambda=1 --regmod=bending_energy --estmov=1 --minmet=0 --splineorder=3 --numprec=double --interp=spline --scale=0 --regrid=0 --verbose

Regards,

Joerg

[muschellij2]

What version of FSL do you have? Run fsl_version or the command line fsl --version

On Fri, Sep 21, 2018 at 6:31 PM JPolzehl ***@***.***> wrote: 1. function topup is currently (version 2.20.3) not in NAMESPACE 2. fslr:::topup("file.nii", "param.txt", out="outfile") creates call ( non existent option infile ) topup --infile=file.nii --datain=param.txt --out=out --warpres=10 --subsamp=1 --fwhm=8 --miter=5 --ssqlambda=1 --regmod=bending_energy --estmov=1 --minmet=0 --splineorder=3 --numprec=double --interp=spline --scale=0 --regrid=0 --verbose instead of ( correct option imain ) topup --imain=file.nii --datain=param.txt --out=out --warpres=10 --subsamp=1 --fwhm=8 --miter=5 --ssqlambda=1 --regmod=bending_energy --estmov=1 --minmet=0 --splineorder=3 --numprec=double --interp=spline --scale=0 --regrid=0 --verbose Regards, Joerg — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#15>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABBnrsIy24n619UiWiinbXkSI3u4Gi8Bks5udWjAgaJpZM4W09cI> .

-- John

[muschellij2]

Try the new version devtools::install_github("muschellij2/fslr")