Error running sct_check_dependencies

SCT
1

Hi. I get the following error when running sct_check_dependencies, after installing SCT on Ubuntu 18.04.3. Could you please advice me on what I should do? Thanks!
~/sct_4.2.1/scripts$ python sct_check_dependencies.py
Traceback (most recent call last):
File “sct_check_dependencies.py”, line 30, in
import sct_utils as sct
File “/home/neurology/sct_4.2.1/scripts/sct_utils.py”, line 43, in
from spinalcordtoolbox import version, sct_dir, data_dir
ImportError: No module named spinalcordtoolbox

2

Hi,

SCT uses its own Python virtual environment (with specific requirements specified in the file $SCT_DIR/requirements.txt). When calling SCT’s scripts via your default Python you are using your own Python environment, hence the error you experienced. To call SCT command, just call the scripts like that:

sct_check_dependencies
3

Thanks for your help!

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