fMRI analysis- ReHo using C-PAC

Software Support
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1

Summary of what happened:

Using code below to calculate and generate ReHo files. Already cleaned time series nifti files (mice data) so only need ReHo. No error returned but no ‘derivatives’ folder generated either. The output folder only had ‘log’, ‘working’ and ‘updated_config’. What’s wrong?

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

singularity run \
/c-pac.sif /4D_dataset.nii /outputs participant --pipeline_file /config.yml

yml content:

regional_homogeneity:
  run: true
  cluster_size: 27

Version:

1.8.7

Environment (Docker, Singularity / Apptainer, custom installation):

Singularity

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

PASTE VALIDATOR OUTPUT HERE

Relevant log outputs (up to 20 lines):

End of subject workflow cpac_sub-mrmdBariatricB342R_ses-iv03

    CPAC run complete:

        Pipeline configuration: cpac-blank-template
        Subject workflow: cpac_sub-mrmdBariatricB342R_ses-iv03
        Elapsed run time (minutes): 0.028964698314666748
        Timing information saved in /home/Desktop/outputs/log/cpac_individual_timing_cpac-blank-template.csv
        System time of start:      2025-01-14 14:47:46
        System time of completion: 2025-01-14 14:47:48
        All expected outputs were generated

Screenshots / relevant information:

2

hi @dsf3243,

It looks like maybe you are trying to use a single non-BIDS file (/4D_dataset.nii ) and no data config. The run will need to contain the following information:

singularity run \
        -B /Users/You/some_folder:/outputs \
        -B /tmp:/tmp \
        -B /Users/You/Documents:/configs \
        fcpindi_c-pac_latest-{date}-{hash value}.img s3://fcp-indi/data/Projects/ADHD200/RawDataBIDS /outputs participant --pipeline-file /configs/pipeline_config.yml

The C-PAC Quickstart Guide has some additional guidance for running cpac, but please let me know if I can clarify any further!