Describe the bug
220531-11:28:48,791 nipype.workflow INFO:
Connecting register_ANTs_anat_to_template...
Traceback (most recent call last):
File "/code/run.py", line 783, in <module>
run_main()
File "/code/run.py", line 764, in run_main
test_config=(1 if args.analysis_level == "test_config" else 0)
File "/code/CPAC/pipeline/cpac_runner.py", line 567, in run
raise e
File "/code/CPAC/pipeline/cpac_runner.py", line 564, in run
p_name, plugin, plugin_args, test_config)
File "/code/CPAC/pipeline/cpac_pipeline.py", line 429, in run_workflow
subject_id, sub_dict, c, p_name, num_ants_cores
File "/code/CPAC/pipeline/cpac_pipeline.py", line 1381, in build_workflow
wf = connect_pipeline(wf, cfg, rpool, pipeline_blocks)
File "/code/CPAC/pipeline/cpac_pipeline.py", line 1051, in connect_pipeline
wf = nb.connect_block(wf, cfg, rpool)
File "/code/CPAC/pipeline/engine.py", line 1252, in connect_block
pipe_x, opt)
File "/code/CPAC/registration/registration.py", line 2204, in register_ANTs_anat_to_template
params, orig='T1w')
File "/code/CPAC/registration/registration.py", line 1486, in ANTs_registration_connector
raise Exception(err_msg)
Exception:
[!] C-PAC says:
You have selected ANTs as your anatomical registration method.
However, no ANTs parameters were specified.
Please specify ANTs parameters properly and try again.
Error: Process completed with exit code 1.
To reproduce
No response
Preconfig
Custom pipeline configuration
No response
Run command
docker run --rm \
--user $(id -u):$(id -g) -v /etc/passwd:/etc/passwd -v /etc/group:/etc/group \
-v $PWD/outputs:/outputs \
ghcr.io/shnizzedy/c-pac:tests_smoke-participant-preconfigs \
/outputs /outputs test_config \
--data_config_file /code/CPAC/resources/configs/test_configs/data-test_human.yml \
--participant_label 101936 2014113 31499 3699991 3884955 NDARAA504CRN NDARAA94ZG5 NDARAB34EWR NDARAB458VK NDARAD481FXF NDARAV894XWD NDARCA186WGH 0025428 0025429 0025448 0025452 0025453 \
--preconfig regtest-4 \
--n_cpus 1
Expected behavior
Preconfig validates
Acceptance criteria
Screenshots
No response
C-PAC version
v1.8.5-dev @ 7ba695ab8eab22185db59c148e53b2aeefc155ae
Container platform
Docker
Docker and/or Singularity version(s)
No response
Additional context
No response
Describe the bug
To reproduce
No response
Preconfig
Custom pipeline configuration
No response
Run command
docker run --rm \ --user $(id -u):$(id -g) -v /etc/passwd:/etc/passwd -v /etc/group:/etc/group \ -v $PWD/outputs:/outputs \ ghcr.io/shnizzedy/c-pac:tests_smoke-participant-preconfigs \ /outputs /outputs test_config \ --data_config_file /code/CPAC/resources/configs/test_configs/data-test_human.yml \ --participant_label 101936 2014113 31499 3699991 3884955 NDARAA504CRN NDARAA94ZG5 NDARAB34EWR NDARAB458VK NDARAD481FXF NDARAV894XWD NDARCA186WGH 0025428 0025429 0025448 0025452 0025453 \ --preconfig regtest-4 \ --n_cpus 1Expected behavior
Preconfig validates
Acceptance criteria
Screenshots
No response
C-PAC version
v1.8.5-dev @ 7ba695ab8eab22185db59c148e53b2aeefc155ae
Container platform
Docker
Docker and/or Singularity version(s)
No response
Additional context
No response