Dear Colm,
that seems very strange. Can I just confirm with you that there are no carriage returns in your command line, and that what I see in the mail is just wrapping?
Jesper
> On 12 Dec 2019, at 09:45, Colm McGinnity <[log in to unmask]> wrote:
>
> Dear Jesper,
>
> Many thanks for gettting back to me.
> The last line simply reads "-h, --help display help info"; please see the text I have copied, below.
>
> I do not see any error message. I have confirmed the files are in the directory, and I have read, write permissions on them all.
> I'm very grateful for your advice, and I hope I haven't made some silly mistake.
> Thanks and best wishes,
> Colm
>
>
>
>
>
> cm15@st-pet048-pc:/data/Colm/fMRI_memory_pilots/fMRI_first3_singlewords_190308_190327/CM/unwarped$ topup --imain=fMRI_memory_long_PA_short_rvols_merged.nii.gz --datain=datain.txt --config=b02b0.cnf --iout=fMRI_memory_long_PA_short_rvols_merged_unwarped --out=fMRI_topup_output
>
> Part of FSL (build 509)
> topup
>
> Usage:
> topup --imain=<some 4D image> --datain=<text file> --config=<text file with parameters> --out=my_topup_results
>
>
> Compulsory arguments (You MUST set one or more of):
> --imain name of 4D file with images
> --datain name of text file with PE directions/times
>
> Optional arguments (You may optionally specify one or more of):
> --out base-name of output files (spline coefficients (Hz) and movement parameters)
> --fout name of image file with field (Hz)
> --iout name of 4D image file with unwarped images
> --logout Name of log-file
> --warpres (approximate) resolution (in mm) of warp basis for the different sub-sampling levels, default 10
> --subsamp sub-sampling scheme, default 1
> --fwhm FWHM (in mm) of gaussian smoothing kernel, default 8
> --config Name of config file specifying command line arguments
> --miter Max # of non-linear iterations, default 5
> --lambda Weight of regularisation, default depending on --ssqlambda and --regmod switches. See user documetation.
> --ssqlambda If set (=1), lambda is weighted by current ssq, default 1
> --regmod Model for regularisation of warp-field [membrane_energy bending_energy], default bending_energy
> --estmov Estimate movements if set, default 1 (true)
> --minmet Minimisation method 0=Levenberg-Marquardt, 1=Scaled Conjugate Gradient, default 0 (LM)
> --splineorder Order of spline, 2->Qadratic spline, 3->Cubic spline. Default=3
> --numprec Precision for representing Hessian, double or float. Default double
> --interp Image interpolation model, linear or spline. Default spline
> --scale If set (=1), the images are individually scaled to a common mean, default 0 (false)
> --regrid If set (=1), the calculations are done in a different grid, default 1 (true)
> -h,--help display help info
> -v,--verbose Print diagonostic information while running
> -h,--help display help info
>
>
>
>
> cm15@st-pet048-pc:/data/Colm/fMRI_memory_pilots/fMRI_first3_singlewords_190308_190327/CM/unwarped$
>
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