Dear developers,
I am trying to run the MAP source code with MONAI Deploy:
monai-deploy exec app -i input/ -o -output/
The first processing step is successful:
(Done performing execution of operator Dcm2NiiOperator)
During the second step:
Going to initiate execution of operator FetalMri3dBrainOperator
the code fails:
No such file or directory: '/home/scripts/docker-recon-brain-auto.bash
Specifically, the problem is located at line 46 of fetal_mri_3d_brain_recon_operator.py, which is "/home/scripts/docker-recon-brain-auto.bash". Indeed, this script exists in /app and /operators within the git clone path on my system.
After hardcoding line 46 to the path pointing to the bash script in /app, the code proceeds until:
RUNNING GLOBAL LOCALISATION ...
but the reconstruction fails, because I do not have MIRTK on my system. In other words,
/home/MIRTK/build/bin/mirtk does not exist.
How can I go about solving this? Do I have to follow the instructions in the section:
[Build and run as MONAI Application Package (MAP)]? I do not have docker on my system, but I do have apptainer. Can I proceed with the latter?
Thank you for creating the tool and for any further assistance!
Dear developers,
I am trying to run the MAP source code with MONAI Deploy:
monai-deploy exec app -i input/ -o -output/The first processing step is successful:
(Done performing execution of operator Dcm2NiiOperator)During the second step:
Going to initiate execution of operator FetalMri3dBrainOperatorthe code fails:
No such file or directory: '/home/scripts/docker-recon-brain-auto.bashSpecifically, the problem is located at line 46 of
fetal_mri_3d_brain_recon_operator.py, which is"/home/scripts/docker-recon-brain-auto.bash". Indeed, this script exists in/appand/operatorswithin the git clone path on my system.After hardcoding line 46 to the path pointing to the bash script in
/app,the code proceeds until:RUNNING GLOBAL LOCALISATION ...but the reconstruction fails, because I do not have MIRTK on my system. In other words,
/home/MIRTK/build/bin/mirtkdoes not exist.How can I go about solving this? Do I have to follow the instructions in the section:
[Build and run as MONAI Application Package (MAP)]? I do not have docker on my system, but I do have apptainer. Can I proceed with the latter?Thank you for creating the tool and for any further assistance!