On 26 Sep 2017, at 15:54, Niels Bergsland <[log in to unmask]> wrote:
Hi Simon,I don't have experience working with data gapped like that.However, I do see that you're missing the "--config=b02b0.cnf" parameter on the command line. So I'd add that and see if you get any further along the way. Also, just to double check, the dwi_rl_lr file is just the b=0 images and does not actually have diffusion-weighted volumes in it as well, right?
Best,Niels
On Tue, Sep 26, 2017 at 4:21 PM, Simon Levy <[log in to unmask]> wrote:
Dear all,
Thank you very much for sharing such useful processing tools, it is of a great help!
However, I am having trouble running topup on an axial diffusion dataset although I think I respected all necessary input parameters. My gut feeling is that the large gap (20mm) between the 3 axial slices making up the dataset is causing trouble to the script. However topup should be able to correct EPI readout-related distortions on such a dataset, either slice-by-slice or interpolating in-between slices.
I am ready to share the data, I think it might be the easiest and most efficient way of fixing this issue, as the error message is not very specific.
Here is the command line used:
topup --imain=dwi_rl_lr.nii.gz --datain=acqparams.txt --out=topup_results --fout=field_estimate --iout=dwi_topup_corrected
And here is the output:
Segmentation fault: 11
Many thanks for your help.
Best regards,
Simon Levy
--
Niels Bergsland
Integration Director / Research Assistant Professor of Neurology
Buffalo Neuroimaging Analysis Center / University at Buffalo
100 High St. Buffalo NY 14203
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