I commented this on this post but I thought it was due to Matlab.
Running sct_label_utils from terminal also gives me the warning from Matplotlib
sct_label_utils -i $T1File -create-viewer 3 -o c3label.nii.gz
Spinal Cord Toolbox (4.3)
/home/sct_4.3/spinalcordtoolbox/gui/widgets.py:12: MatplotlibDeprecationWarning:
The matplotlib.backends.backend_qt4agg backend was deprecated in Matplotlib 3.3 and will be removed two minor releases later.
from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
Since it’s a warning I can still select c3 from the GUI and everything runs smoothly.
Running ``sct_check_dependencies` gives me
sct_check_dependencies
--
Spinal Cord Toolbox (4.3)
SCT info:
- version: 4.3
- path: /home/sct_4.3
OS: linux (Linux-5.3.0-62-generic-x86_64-with-debian-buster-sid)
CPU cores: Available: 12, Used by SCT: 12
RAM: MemTotal: 131596272 kB
total usado libre compartido búfer/caché disponible
Memoria: 128511 9071 1654 405 117785 117812
Swap: 975 2 973
Check Python executable.............................[OK]
Using bundled python 3.6.12 |Anaconda, Inc.| (default, Sep 8 2020, 23:10:56)
[GCC 7.3.0] at /home/sct_4.3/python/envs/venv_sct/bin/python
Check if torch (1.5.0+cpu) is installed.............[WARNING] (1.6.0 != 1.5.0+cpu mandated version))
Check if torchvision (0.6.0+cpu) is installed.......[WARNING] (0.7.0 != 0.6.0+cpu mandated version))
All the other dependencies are [OK]. Can this difference in torch and torchvision be the reason?
This suggests that you’ve installed SCT two times on the same system, but not at the same location, and the PATH seems to be incorrectly set. This is likely the reason why you have these warnings.
I suggest you install a fresh version, and say “yes” to everything (ie: .bashrc edit).
Could you please copy/paste the entire Terminal output showing your installation (starting from the syntax you run), so we can figure out what went wrong? You can do it either from 5.0.0 or from the master branch.
i think it’s related to the viewer function/option
extop@:/mnt/aran/testing/001_1$ sct_deepseg_sc -i n4_T1.nii -centerline viewer -c t1
--
Spinal Cord Toolbox (5.0.0)
Config deepseg_sc:
Centerline algorithm: viewer
Brain in image: True
Kernel dimension: 2d
Contrast: t1
Threshold: 0.15
Creating temporary folder (/tmp/sct-20201113075251.758061-ygir0amh)
Reorient the image to RPI, if necessary...
Finding the spinal cord centerline...
/home/extop/sct_5.0.0/spinalcordtoolbox/gui/widgets.py:10: MatplotlibDeprecationWarning:
The matplotlib.backends.backend_qt4agg backend was deprecated in Matplotlib 3.3 and will be removed two minor releases later.
from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
Cropping the image around the spinal cord...
Normalizing the intensity...
Segmenting the spinal cord using deep learning on 2D patches...
Traceback (most recent call last):
File "/home/extop/sct_5.0.0/scripts/sct_deepseg_sc.py", line 208, in <module>
main()
File "/home/extop/sct_5.0.0/scripts/sct_deepseg_sc.py", line 192, in main
threshold_seg=threshold, remove_temp_files=remove_temp_files, verbose=verbose)
File "/home/extop/sct_5.0.0/spinalcordtoolbox/deepseg_sc/core.py", line 509, in deep_segmentation_spinalcord
im_in=im_norm_in)
File "/home/extop/sct_5.0.0/spinalcordtoolbox/deepseg_sc/core.py", line 350, in segment_2d
seg_model.load_weights(model_fname)
File "/home/extop/sct_5.0.0/python/envs/venv_sct/lib/python3.6/site-packages/keras/engine/topology.py", line 2656, in load_weights
f, self.layers, reshape=reshape)
File "/home/extop/sct_5.0.0/python/envs/venv_sct/lib/python3.6/site-packages/keras/engine/topology.py", line 3328, in load_weights_from_hdf5_group
original_keras_version = f.attrs['keras_version'].decode('utf8')
AttributeError: 'str' object has no attribute 'decode'
extop@:/mnt/aran/testing/001_1$
Probably now it is not the best time to solve this, since the “no attribute” problem also exists.
I’ve checked and i can tell you that using centerline -cnn the program jumps to the second error directly