problem to openneurodesk applicatiion

[Aljohani2]

Dear Neurodesk Dvelopers Team,

Thank you for developing this great platforms. I installd Docker and Neurodesk apps for my Windows desktop. I have trying for over weeks to so as no previous IT experience. After all, I could open the nurodesk app and test some commands from mrtrix e.g mrconvertt and able to tconvert the dicom file but I cannot visualise or view it via mrview command. Also, I cannot access or open fsleyes and spinalcord toolbox. Could you please help me in this issue and guide me hw it could be solved?

Please see output for testing sct help command:

(base) jovyan@neurodesktop-2024-05-25:~$ sct_deepseg
^CTraceback (most recent call last):
File "/opt/spinalcordtoolbox-5.7/bin/sct_deepseg", line 33, in
sys.exit(load_entry_point('spinalcordtoolbox', 'console_scripts', 'sct_deepseg')())
File "/opt/spinalcordtoolbox-5.7/bin/sct_deepseg", line 25, in importlib_load_entry_point
return next(matches).load()
File "/opt/spinalcordtoolbox-5.7/python/envs/venv_sct/lib/python3.7/site-packages/importlib_metadata/init.py", line 203, in load
module = import_module(match.group('module'))
File "/opt/spinalcordtoolbox-5.7/python/envs/venv_sct/lib/python3.7/importlib/init.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "", line 1006, in _gcd_import
File "", line 983, in _find_and_load
File "", line 953, in _find_and_load_unlocked
File "", line 219, in _call_with_frames_removed
File "", line 1006, in _gcd_import
File "", line 983, in _find_and_load
File "", line 953, in _find_and_load_unlocked
File "", line 219, in _call_with_frames_removed
File "", line 1006, in _gcd_import
File "", line 983, in _find_and_load
File "", line 967, in _find_and_load_unlocked
File "", line 677, in _load_unlocked
File "", line 728, in exec_module
File "", line 219, in _call_with_frames_removed
File "/opt/spinalcordtoolbox-5.7/spinalcordtoolbox/init.py", line 1, in
from .utils import version, sct_dir, data_dir, deepseg_dir # noqa: F401
File "/opt/spinalcordtoolbox-5.7/spinalcordtoolbox/utils/init.py", line 1, in
from .fs import * # noqa: F401, F403
File "/opt/spinalcordtoolbox-5.7/spinalcordtoolbox/utils/fs.py", line 11, in
from .sys import printv
File "/opt/spinalcordtoolbox-5.7/spinalcordtoolbox/utils/sys.py", line 12, in
import smtplib
File "/opt/spinalcordtoolbox-5.7/python/envs/venv_sct/lib/python3.7/smtplib.py", line 182, in
import ssl
File "", line 983, in _find_and_load
File "", line 967, in _find_and_load_unlocked
File "", line 677, in _load_unlocked
File "", line 724, in exec_module
File "", line 818, in get_code
File "", line 916, in get_data
KeyboardInterrupt

Many thanks in advance,

Ghazi aljohani

[stebo85]

Which version of the spinal cord toolbox are you using ? Can you describe step by step what you are doing and also provide some example data?

[stebo85]

Dear @Aljohani2

Can you if you analysis works on play.neurodesk.org to exclude if anything is wrong with your setup? It looks like you are trying to run spinalcordtoolbox-5.7. Did you load this using "module load spinalcordtoolbox/5.7"? You need to provide data to the command you are running - here is an example for the sct: https://www.neurodesk.org/example-notebooks/structural_imaging/sct_toolbox_example.html