 |
 |
Hi Jesper, Useful to know about the diminishing returns of the extra b0s; I've adjusted my inputs accordingly to avoid this taking an extraordinarily long time (got about 300 inputs!). Thanks very much for your reply, Iain On Wed, 20 Feb 2019 at 16:26, Jesper Andersson < [log in to unmask]> wrote: > 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 > > > > ######################################################################## > > > > To unsubscribe from the FSL list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 > > ######################################################################## > > To unsubscribe from the FSL list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 > -- Dr Iain Croall, PhD Postdoctoral Researcher University of Sheffield Dept. Infection, Immunity and Cardiovascular Disease Academic Unit of Radiology email: [log in to unmask] phone: 0114 2159151 ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1