Hi everyone,
Please, I’m trying to measure ALFF, fALFF, and ReHo on data that’s already been preprocessed with fMRIPrep using C-PAC via Docker. I’m running the latest C-PAC Docker image (fcpindi/c-pac:latest)
Docker version
26.1.3 (build 26.1.3-0ubuntu1~24.04.1)
I’m launching CPAC with the following command:
docker run -i --rm \
-v /home/oumayma/Downloads/fmriprep_control:/fmriprep_control \
-v /home/oumayma/Downloads/cpac_outputs:/outputs \
-v /home/oumayma/Downloads/data_config_fmriprep_data_config.yml:/data_config.yml \
-v /home/oumayma/Downloads/pipeline_config.yml:/pipeline_config.yml \
fcpindi/c-pac:latest /fmriprep_control /outputs participant \
--data-config-file /data_config.yml \
--pipeline-file /pipeline_config.yml
My custom data configuration file (data_config_fmriprep_data_config.yml) is set up as follows:
dataFormat: 'Custom'
bidsBaseDir: /data/fmriprep_control
outputSubjectListLocation: /data
subjectListName: fmriprep_data_config
brain_mask_template: None
anatomicalTemplate: /data/fmriprep_control/{participant}/anat/{participant}_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz
functionalTemplate: /data/fmriprep_control/{participant}/func/{participant}_task-rest_acq-rest_run-1_*_desc-preproc_bold.nii.gz
freesurferTemplate: None
However, when I try to generate the data configuration file by running:
docker run -it --rm --entrypoint bash -v /home/oumayma/Downloads:/data fcpindi/c-pac:latest
and then executing:
cpac utils data-config build /data/data_settings.yml
I encounter the following error:
/usr/share/fsl/6.0/bin/cpac:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
__import__('pkg_resources').require('CPAC==1.8.7.dev1')
Generating data configuration file..
Traceback (most recent call last):
File "/usr/share/fsl/6.0/bin/cpac", line 7, in <module>
exec(compile(f.read(), __file__, 'exec'))
File "/code/scripts/cpac", line 5, in <module>
main()
File "/usr/share/fsl/6.0/lib/python3.10/site-packages/click/core.py", line 1157, in __call__
return self.main(*args, **kwargs)
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
It appears that the error occurs during the configuration build process, specifically with an issue related to freesurfer_glob.
Any guidance or suggestions to solve it would be greatly appreciated!
AND could you please provide a guide or tutorial on how to work with C-PAC on Colab?
Thanks !