Dear Iain,

>
> I'm processing some DTI information and using topup in the preprocessing to estimate the fieldmaps for geometric distortion correction. My question is that it's been running for > 2 hours now on one dataset and it still hasn't exited. I've used topup before on the same computer / FSL installation and don't remember it taking anything like this long (though admittedly that was on a dataset with only 2 b0s of opposite blips; currently I've got 8 b0s being processed). The logfile hasn't got anything that looks like an error in it, and seems to have stalled at the current point (it's been sitting at the same stage for at least an hour when I first checked it). I'll paste the log file into the bottom of this email for reference.
>
> Is it normal for it to take this long perhaps due to the number of b0 images? Or does it sound like it's hit a snag?
>
> The topup data is 8 b0 images, the first 5 are A >> P (image appears displaced "downwards"), and the last 3 are P >> A (displaced "upwards"). I got the total readout time from the .json file generated in DICOM conversion using dcm2niix. I'm 99% certain I've set up the acquisition parameters correctly:

the execution time scales pretty much linearly with the number of volumes you have in your --imain file. My advice is to use only a single pair since one sees very little, if any, improvement of results by using more than that. We still recommend acquiring more than one (3-5) b0, but that is to make sure that you have at least one b0 for each direction that is not damaged by intra-volume movement.

Jesper

>
> 0 -1 0 0.0690115 (x5)
> 0 1 0 0.0690115 (x3)
>
> Thanks in advance for any advice,
> Iain
>
>
> #     name of 4D file with images
> --imain=topup_b0s.nii.gz
> # name of text file with PE directions/times
> --datain=/mnt/hgfs/SHARED_FILES/Biobank/topup_acq_pars.txt
> #     base-name of output files (spline coefficients (Hz) and movement parameters)
> --out=1042018_topped_up
> #     name of image file with field (Hz)
> --fout=field
> #     name of 4D image file with unwarped images
> --iout=unwarped_images
> # (approximate) resolution (in mm) of warp basis for the different sub-sampling levels, default 10
> --warpres=20,16,14,12,10,6,4,4,4
> # sub-sampling scheme, default 1
> --subsamp=2,2,2,2,2,1,1,1,1
> #     FWHM (in mm) of gaussian smoothing kernel, default 8
> --fwhm=8,6,4,3,3,2,1,0,0
> #     Max # of non-linear iterations, default 5
> --miter=5,5,5,5,5,10,10,20,20
> # Weight of regularisation, default depending on --ssqlambda and --regmod switches. See user documetation.
> --lambda=0.005,0.001,0.0001,1.5e-05,5e-06,5e-07,5e-08,5e-10,1e-11
> # If set (=1), lambda is weighted by current ssq, default 1
> --ssqlambda=1
> # Estimate movements if set, default 1 (true)
> --estmov=1,1,1,1,1,0,0,0,0
> # Minimisation method 0=Levenberg-Marquardt, 1=Scaled Conjugate Gradient, default 0 (LM)
> --minmet=0,0,0,0,0,1,1,1,1
> # Model for regularisation of warp-field [membrane_energy bending_energy], default bending_energy
> --regmod=bending_energy
> # Order of spline, 2->Qadratic spline, 3->Cubic spline. Default=3
> --splineorder=3
> # Precision for representing Hessian, double or float. Default double
> --numprec=double
> # Image interpolation model, linear or spline. Default spline
> --interp=spline
> #     If set (=1), the images are individually scaled to a common mean, default 0 (false)
> --scale=1
> #     If set (=1), the calculations are done in a different grid, default 1 (true)
> --regrid=1
>
> ########################################################################
>
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