AttributeError: np.NaN was removed in the NumPy 2.0 release. Use np.nan instead.

[kavandeloo97]

Getting this error when trying to use visualqc_freesurfer -h:

(base) admin@Katies-iMac scripts % visualqc_freesurfer -h
Traceback (most recent call last):
File "/Users/admin/miniconda3/bin/visualqc_freesurfer", line 5, in
from visualqc.freesurfer import main
File "/Users/admin/miniconda3/lib/python3.11/site-packages/visualqc/init.py", line 24, in
from visualqc.readers import (gather_freesurfer_data, read_aparc_stats_in_hemi,
File "/Users/admin/miniconda3/lib/python3.11/site-packages/visualqc/readers.py", line 10, in
from visualqc import config as cfg
File "/Users/admin/miniconda3/lib/python3.11/site-packages/visualqc/config.py", line 180, in
line_break = [np.NaN, np.NaN]
^^^^^^
File "/Users/admin/miniconda3/lib/python3.11/site-packages/numpy/init.py", line 400, in getattr
raise AttributeError(
AttributeError: np.NaN was removed in the NumPy 2.0 release. Use np.nan instead.
(base) admin@Katies-iMac scripts % vqcfs -h
Traceback (most recent call last):
File "/Users/admin/miniconda3/bin/vqcfs", line 5, in
from visualqc.freesurfer import main
File "/Users/admin/miniconda3/lib/python3.11/site-packages/visualqc/init.py", line 24, in
from visualqc.readers import (gather_freesurfer_data, read_aparc_stats_in_hemi,
File "/Users/admin/miniconda3/lib/python3.11/site-packages/visualqc/readers.py", line 10, in
from visualqc import config as cfg
File "/Users/admin/miniconda3/lib/python3.11/site-packages/visualqc/config.py", line 180, in
line_break = [np.NaN, np.NaN]
^^^^^^
File "/Users/admin/miniconda3/lib/python3.11/site-packages/numpy/init.py", line 400, in getattr
raise AttributeError(
AttributeError: np.NaN was removed in the NumPy 2.0 release. Use np.nan instead.

[raamana]

Thanks @kavandeloo97 for reporting the issue - I will take a look and try to fix it asap. if you need it in the meanwhile, just downgrade your numpy version for now e.g., use one version earlier with pip install numpy==1.26.4 and try rerun visualqc?