Open nimzodisaster opened 7 months ago
Hi @nimzodisaster, thanks for reporting!
What does
cpac version
say?
cpac (convenience wrapper) version 1.8.6 C-PAC version v1.8.6.dev1 running on Docker version 24.0.7
Try replacing
freesurfer_dir: None
in your data_settings.yml
with
freesurfer_dir:
That worked. I guess it misreads that key as a string instead of the None keyword. Thanks!
Great, glad it worked!
We can keep this issue open though, to make this clearer. I think this is actually a design flaw in the template data_settings.yml
since the ways to encode None
in YAML are [, null, Null, NULL, ~]
(not "None
")
Describe the bug
I am trying to build the data_settings
I receive the following error: `(rs) jlee38@:/mnt/drive/rs$ cpac utils data-config build ./data_settings.yml Loading 🐳 Docker .... .... Traceback (most recent call last): File "/code/run.py", line 827, in
Generating data configuration file.. run_main() File "/code/run.py", line 367, in run_main main.main(args=sys.argv[sys.argv.index('--') + 1:]) File "/usr/share/fsl/6.0/lib/python3.10/site-packages/click/core.py", line 1078, in main rv = self.invoke(ctx) File "/usr/share/fsl/6.0/lib/python3.10/site-packages/click/core.py", line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/usr/share/fsl/6.0/lib/python3.10/site-packages/click/core.py", line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/usr/share/fsl/6.0/lib/python3.10/site-packages/click/core.py", line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/usr/share/fsl/6.0/lib/python3.10/site-packages/click/core.py", line 1434, in invoke return ctx.invoke(self.callback, *ctx.params) File "/usr/share/fsl/6.0/lib/python3.10/site-packages/click/core.py", line 783, in invoke return __callback(args, **kwargs) File "/code/CPAC/main.py", line 356, in build run(data_settings_file) File "/code/CPAC/utils/build_data_config.py", line 1849, in run data_dct = get_nonBIDS_data(settings_dct['anatomicalTemplate'], File "/code/CPAC/utils/build_data_config.py", line 1589, in get_nonBIDS_data for dir in os.listdir(str(os.path.dirname(freesurfer_glob))): UnboundLocalError: local variable 'freesurfer_glob' referenced before assignment ` Attached is the data_settings file I used data_settings.yml.txt
To reproduce
No response
Preconfig
Custom pipeline configuration
No response
Run command
No response
Expected behavior
I expect to get subject configs file
Acceptance criteria
successfully execute
Screenshots
No response
C-PAC version
1.8.6.dev1
Container platform
Docker
Docker and/or Singularity version(s)
24.0.7
Additional context
No response