Dear Matteo,
I'm trying to run eddy_squad without specifying any (optional) grouping variables and I'm getting the following error message(s):
[...]$ eddy_squad -o eddy_squad_outputs .../eddy_quad_folders.txt
Generating group database...
Group database generated and stored. Writing group QC report...
Traceback (most recent call last):
File "/share/pkg/fsl/6.0/install/bin/eddy_squad", line 40, in <module>
main(args.list, args.grouping, args.group_db, args.update, args.output_dir)
File "/share/pkg/fsl/6.0/install/fslpython/envs/fslpython/lib/python3.6/site-packages/eddy_qc/SQUAD/squad.py", line 99, in main
squad_group.main(pp, db, group, None)
File "/share/pkg/fsl/6.0/install/fslpython/envs/fslpython/lib/python3.6/site-packages/eddy_qc/SQUAD/squad_group.py", line 240, in main
seaborn.violinplot(data=db['qc_cnr'][:,1:], scale='width', width=0.5, palette='Set3', linewidth=1, inner='point', ax=ax2_02)
File "/share/pkg/fsl/6.0/install/fslpython/envs/fslpython/lib/python3.6/site-packages/seaborn/categorical.py", line 2364, in violinplot
color, palette, saturation)
File "/share/pkg/fsl/6.0/install/fslpython/envs/fslpython/lib/python3.6/site-packages/seaborn/categorical.py", line 559, in __init__
self.estimate_densities(bw, cut, scale, scale_hue, gridsize)
File "/share/pkg/fsl/6.0/install/fslpython/envs/fslpython/lib/python3.6/site-packages/seaborn/categorical.py", line 625, in estimate_densities
kde, bw_used = self.fit_kde(kde_data, bw)
File "/share/pkg/fsl/6.0/install/fslpython/envs/fslpython/lib/python3.6/site-packages/seaborn/categorical.py", line 712, in fit_kde
kde = stats.gaussian_kde(x, bw)
File "/share/pkg/fsl/6.0/install/fslpython/envs/fslpython/lib/python3.6/site-packages/scipy/stats/kde.py", line 172, in __init__
self.set_bandwidth(bw_method=bw_method)
File "/share/pkg/fsl/6.0/install/fslpython/envs/fslpython/lib/python3.6/site-packages/scipy/stats/kde.py", line 499, in set_bandwidth
self._compute_covariance()
File "/share/pkg/fsl/6.0/install/fslpython/envs/fslpython/lib/python3.6/site-packages/scipy/stats/kde.py", line 510, in _compute_covariance
self._data_inv_cov = linalg.inv(self._data_covariance)
File "/share/pkg/fsl/6.0/install/fslpython/envs/fslpython/lib/python3.6/site-packages/scipy/linalg/basic.py", line 947, in inv
a1 = _asarray_validated(a, check_finite=check_finite)
File "/share/pkg/fsl/6.0/install/fslpython/envs/fslpython/lib/python3.6/site-packages/scipy/_lib/_util.py", line 238, in _asarray_validated
a = toarray(a)
File "/share/pkg/fsl/6.0/install/fslpython/envs/fslpython/lib/python3.6/site-packages/numpy/lib/function_base.py", line 1233, in asarray_chkfinite
"array must not contain infs or NaNs")
ValueError: array must not contain infs or NaNs
I've also tried running the command using the same version of the eddy_qc tools patched to our FSL5.0.10 install and I'm getting a very similar error message:
[...]$ eddy_squad -o eddy_squad_outputs .../eddy_quad_folders.txt
Generating group database...
Group database generated and stored. Writing group QC report...
Traceback (most recent call last):
File "/share/pkg/fsl/5.0.10-patched/install/eddy_qc-master/eddy_qc/scripts/eddy_squad", line 40, in <module>
main(args.list, args.grouping, args.group_db, args.update, args.output_dir)
File "/share/pkg/fsl/5.0.10/install/fslpython/envs/fslpython/lib/python3.5/site-packages/eddy_qc-1.0.0-py3.5.egg/eddy_qc/SQUAD/squad.py", line 99, in main
File "/share/pkg/fsl/5.0.10/install/fslpython/envs/fslpython/lib/python3.5/site-packages/eddy_qc-1.0.0-py3.5.egg/eddy_qc/SQUAD/squad_group.py", line 240, in main
File "/share/pkg/fsl/5.0.10/install/fslpython/envs/fslpython/lib/python3.5/site-packages/seaborn-0.9.0-py3.5.egg/seaborn/categorical.py", line 2387, in violinplot
color, palette, saturation)
File "/share/pkg/fsl/5.0.10/install/fslpython/envs/fslpython/lib/python3.5/site-packages/seaborn-0.9.0-py3.5.egg/seaborn/categorical.py", line 564, in __init__
self.estimate_densities(bw, cut, scale, scale_hue, gridsize)
File "/share/pkg/fsl/5.0.10/install/fslpython/envs/fslpython/lib/python3.5/site-packages/seaborn-0.9.0-py3.5.egg/seaborn/categorical.py", line 630, in estimate_densities
kde, bw_used = self.fit_kde(kde_data, bw)
File "/share/pkg/fsl/5.0.10/install/fslpython/envs/fslpython/lib/python3.5/site-packages/seaborn-0.9.0-py3.5.egg/seaborn/categorical.py", line 717, in fit_kde
kde = stats.gaussian_kde(x, bw)
File "/share/pkg/fsl/5.0.10/install/fslpython/envs/fslpython/lib/python3.5/site-packages/scipy/stats/kde.py", line 171, in __init__
self.set_bandwidth(bw_method=bw_method)
File "/share/pkg/fsl/5.0.10/install/fslpython/envs/fslpython/lib/python3.5/site-packages/scipy/stats/kde.py", line 498, in set_bandwidth
self._compute_covariance()
File "/share/pkg/fsl/5.0.10/install/fslpython/envs/fslpython/lib/python3.5/site-packages/scipy/stats/kde.py", line 509, in _compute_covariance
self._data_inv_cov = linalg.inv(self._data_covariance)
File "/share/pkg/fsl/5.0.10/install/fslpython/envs/fslpython/lib/python3.5/site-packages/scipy/linalg/basic.py", line 658, in inv
a1 = _asarray_validated(a, check_finite=check_finite)
File "/share/pkg/fsl/5.0.10/install/fslpython/envs/fslpython/lib/python3.5/site-packages/scipy/_lib/_util.py", line 228, in _asarray_validated
a = toarray(a)
File "/share/pkg/fsl/5.0.10/install/fslpython/envs/fslpython/lib/python3.5/site-packages/numpy/lib/function_base.py", line 1033, in asarray_chkfinite
"array must not contain infs or NaNs")
ValueError: array must not contain infs or NaNs
Any help would be much appreaciated.
Best,
Matthias
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