🐛 Error during 'cpac utils data-config build ./data_settings.yml' re reference before assignment

[nimzodisaster]

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

• default
• abcd-options
• anat-only
• blank
• ccs-options
• fmriprep-options
• fx-options
• monkey
• monkey-ABCD
• ndmg
• nhp-macaque
• preproc
• rbc-options
• rodent

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

[shnizzedy]

Hi @nimzodisaster, thanks for reporting!

What does

cpac version

say?

[nimzodisaster]

cpac (convenience wrapper) version 1.8.6
C-PAC version v1.8.6.dev1 running on Docker version 24.0.7

[shnizzedy]

Try replacing

freesurfer_dir: None

in your data_settings.yml with

freesurfer_dir:

[nimzodisaster]

That worked. I guess it misreads that key as a string instead of the None keyword.
Thanks!

[shnizzedy]

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")