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!

3

Hi @tamsinrogers,

Thanks a lot for the reply. If using the standard pipeline format, does it mean I have to start with BIDS? My data has already gone through the preprocessing procedures and right now are cleaned time series. Wonder if I can do the ReHo step only?

4

Hi @dsf3243,

If your data is not in BIDS format, it will need to be reorganized to follow the following structure:

/subjects/
  sub-01/
    func/
      sub-01_task-rest_bold.nii.gz

If using non-BIDS data, you’ll need to set up a custom data config file so C-PAC can read your data.

To do the ReHo step only, you can create a custom pipeline configuration by disabling the preprocessing steps you have already run on your data and enabling only the ReHo step.

Let me know if I can help with any of these steps!

5

Hi @tamsinrogers,

Thank you again for the reply. I’ll test a bit with the configs settings. Just a quick one if I may, since I’m using already processed time series data, I assume this '-B /tmp:/tmp ' step for template can be skipped?

6

Hi @dsf3243,

Yes, that should be fine, as long as you are specifying the locations for raw data, output, and config.

Let me know how it goes!