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Hi Mark, It seems as if it does not manage to correctly generate the averaged b0 volume. If you look inside the output .qc folder after it crashes, do you see the avg_b0.nii.gz file? If so, what are its dimensions? Cheers, Matteo > On 9 Jan 2019, at 21:16, Mark Grier <[log in to unmask]> wrote: > > I am attempting to run eddy_quad and all of my data sets give me the following error. Can anyone help me figure out where the problem is originating? > > eddy_quad eddy_unwarped -idx index.txt -par acqparams.txt -m nodif_brain_mask.nii.gz -b bvals > found b-shell of 16 orientations with b-value 20.000000 > found b-shell of 108 orientations with b-value 1000.000000 > found b-shell of 106 orientations with b-value 2000.000000 > Traceback (most recent call last): > File "/usr/local/fsl6/bin/eddy_quad", line 52, in <module> > main(args.eddyBase, args.eddyIdx, args.eddyParams, args.mask, args.bvals, args.bvecs, args.output_dir, args.field, args.slspec, args.verbose) > File "/usr/local/fsl6/fslpython/envs/fslpython/lib/python3.6/site-packages/eddy_qc/QUAD/quad.py", line 359, in main > quad_avg_maps.main(pp, data, eddyOutput) > File "/usr/local/fsl6/fslpython/envs/fslpython/lib/python3.6/site-packages/eddy_qc/QUAD/quad_avg_maps.py", line 40, in main > i_max = np.round(np.mean(vol[:,:,:][data['mask'] != 0.0])+3*np.std(vol[:,:,:][data['mask'] != 0.0])) > IndexError: too many indices for array > > ######################################################################## > > 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