Error with C-PAC data configuration file building

Software Support
,
1

Summary of what happened:

I prepared my data_settings.ymal file and I am trying to create the data configuration file but I keep receiving this error on that:

usage: run. py
19
--analysis_lev
20
[-h] [--ptpeline Flle PIPELINE FILE] t- group File GROUP FILE
-data_config_file DATA_CONFIG_FILE] [-•preconfig PRECONFIG]
21
-aws_input_creds AWS _INPUT_CREDS]
-aws_output_
_Creds AWS_OUTPUT_CREDS] I--n_cpus N_CPUS]
[•-mem_mb MEM_MB] L--mem gb MEM_GB]
runtime_usage RUNTIME_USAGE]
runtime_buffer RUNTIME BUFFER]
num_ants_threads NUM_ANTS_THREADS]
•random_seed RANDOM_SEED]
save working_dir [SAVE_WORKING_DIR]] [--save_workflow]
I--fail_fast FAIL_FASTI
-participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL• JJ
-participant
_ndx PARTICIPANT
-NDX] T- T1w_label T1W_LABEL]
_Label BOLD_LABEL [BOLD_LABEL •• •11 [-v]
_validator.
_config BIDS_VALIDATOR _CONFIG]
[--skip_bids_validator] [- -anat_only] [--tracking_opt-out]
[- -monitoring]
bids_dir output_dir (participant, group, test.
_config, cli}
run.py: error: the following arguments are required: output_dir, analysis_level

Command used (and if a helper script was used, a link to the helper script or the command generated):

docker run -i --rm - user Sid -u) \
v /path/to/data_config: /scratch\
W=" /scratch" \
fepindi/c-pac: latest\
SBIDS_DIR SOUTPUTS_DIR
cli -- utils data-config build \
/home/nsa-Lab/Desktop/configurationfiles/data_settings.yml
output_dir /home/nsa- lab/Desktop/configurationftles
analysis_level participant

Version:

Environment (Docker, Singularity, custom installation):

I am using docker and my operating system is Ubuntu 22.04 and I installed docker through terminal.

Data formatted according to a validatable standard? Please provide the output of the validator:

Relevant log outputs (up to 20 lines):

Screenshots / relevant information:

2

Hi @maryam.riazi and welcome to neurostars!

Can you use this syntax to run CPAC? C-PAC Quickstart - C-PAC 1.8.5 Beta documentation

Best,
Steven

3

Hi Steven
Thank for your reply.
now I am trying to run this code:
capc --platform docker --tag latest run /home/nsa-lab/bids /home/nsa-lab/outputs participant --preconfig default

In the bids directory:

mgh: 
  sub-01100:
     anat:
       anat.nii.gz
     func: 
       fuc.nii.gz

right now I am getting this error:
<OSError: Didn’t find any files in /home/nsa-lab/Desktop/bids. Please verif y that the path is typed correctly, that you have read access to the directory, and that it is not empty>

4

Hi @maryam.riazi

This does not look like a BIDS valid dataset. You can refer to the BIDS starter kit for how to set up your data in BIDS format.

Best,
Steven

5

You can refer to the BIDS starter kit for how to set up your data in BIDS format.

Alternatively, you can use a data configuration file if you want to use non-BIDS input data with C-PAC.