Hi Hilmar,
eddy_squad expects either N integers or floating numbers to generate extra quality metric plots based on specific groups (e.g., males/females) or continuous variables (e.g., age), where N is the number of subjects you have. It seems to me that you have v_1 … v_n (i.e., strings) in your grouping variable text file.
Keep in mind that you do not need to specify the --grouping flag if you do not want to generate such extra plots.
Hope this helps, cheers,
Matteo
> On 29 Jul 2019, at 10:45, Hilmar Sigurdsson <[log in to unmask]> wrote:
>
> Hi All,
>
> I am trying to run eddy_squad to get an overall quality assurance but I keep getting an error:
> Generating group database...
> Group database generated and stored. Writing group QC report...
> Traceback (most recent call last):
> File "/mnt/nfs/home/nhs119/bin/fsl/bin/eddy_squad", line 42, in <module>
> main(args.list, args.grouping, args.group_db, args.update, args.output_dir)
> File "/mnt/nfs/home/nhs119/bin/fsl/fslpython/envs/fslpython/lib/python3.7/site-packages/eddy_qc/SQUAD/squad.py", line 107, in main
> squad_group.main(pp, db, group, None)
> File "/mnt/nfs/home/nhs119/bin/fsl/fslpython/envs/fslpython/lib/python3.7/site-packages/eddy_qc/SQUAD/squad_group.py", line 47, in main
> g = seaborn.distplot(grp[grp.dtype.names[0]][1:], vertical=True, bins=np.arange(-1.5+round(min(grp[grp.dtype.names[0]][1:])),1.5+round(max(grp[grp.dtype.names[0]][1:]))), norm_hist=False, kde=False, ax=ax1_00)
> TypeError: ufunc 'rint' not supported for the input types, and the inputs could not be safely coerced to any supported types according to the casting rule ''safe''
>
> I'm running this on a CentOS 7
> My command is:
> eddy_squad ${QClist} --grouping=${PRJDIR}/subjects_all.txt --update --output-dir=${PRJDIR}/SQUAD_out_${now}
>
> Interestingly, this runs fine if I skip the --grouping flag. Therefore, I suspect I am not setting upt the grouping txt file correctly.
>
> subjects_all.txt:
> SubList
> 0
> v_1
> v_2
> v_3
> .
> .
> v_n where n is the number of the last subject.
>
> Any help would be appreciated. Thank you!
> Hilmar
>
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