CPAC: None of Listed Resources In Node Block Exist In Resource Pool

Software Support
1

Summary of what happened:

I am trying to modify the segmentation method from FSL-BET to FreeSurfer in the CPAC default pipeline. However, I get an error related to node block when I try to make this change. CPAC default pipeline works without issues, but having challenges with making the segmentation change.

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

cpac run GU_28830 OUTPUT participant --pipeline-file cpac_1_24.yml

Version:

CPAC 1.8.6

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

Singularity run on a HPC

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

Running BIDS validator
#### Running C-PAC
Number of participants to run in parallel: 1
Input directory: /vf/users/NNU_NDData_Projs/ASD_Targeting/MRI_Raw/ABIDE_2/ABIDE_2_BIDS/GU_28830
Output directory: /vf/users/NNU_NDData_Projs/ASD_Targeting/MRI_Raw/ABIDE_2/ABIDE_2_BIDS/OUTPUT_1_24/output
Working directory: /vf/users/NNU_NDData_Projs/ASD_Targeting/MRI_Raw/ABIDE_2/ABIDE_2_BIDS/OUTPUT_1_24/working
Log directory: /vf/users/NNU_NDData_Projs/ASD_Targeting/MRI_Raw/ABIDE_2/ABIDE_2_BIDS/OUTPUT_1_24/log
Remove working directory: True
Available memory: 1.0 (GB)
Available threads: 1
Number of threads for ANTs: 1
Parsing /vf/users/NNU_NDData_Projs/ASD_Targeting/MRI_Raw/ABIDE_2/ABIDE_2_BIDS/GU_28830..
Starting participant level processing
Run called with config file /vf/users/NNU_NDData_Projs/ASD_Targeting/MRI_Raw/ABIDE_2/ABIDE_2_BIDS/OUTPUT_1_24/log/pipeline_cpac-default-pipeline/sub-GU28830_ses-1/cpac_pipeline_config_9c8e9d7f_2024-01-24T10-11-26Z.yml
240124-10:11:30,214 nipype.workflow INFO:

Relevant log outputs (up to 20 lines):

240124-10:11:31,386 nipype.workflow ERROR:
	 Building workflow failed
Traceback (most recent call last):
  File "/code/CPAC/pipeline/cpac_pipeline.py", line 1497, in build_workflow
    wf = connect_pipeline(wf, cfg, rpool, pipeline_blocks)
  File "/code/CPAC/pipeline/cpac_pipeline.py", line 1123, in connect_pipeline
    wf = nb.connect_block(wf, cfg, rpool)
  File "/code/CPAC/pipeline/engine.py", line 1468, in connect_block
    for pipe_idx, strat_pool in rpool.get_strats(
  File "/code/CPAC/pipeline/engine.py", line 552, in get_strats
    raise LookupError('\n\n[!] C-PAC says: None of the listed '
LookupError: When trying to connect one of the node blocks ['tissue_seg_fsl_fast', 'tissue_seg_ants_prior', 'tissue_seg_freesurfer'] to workflow 'cpac_sub-GU28830_ses-1' after node block 'register_symmetric_FSL_anat_to_template': 

[!] C-PAC says: None of the listed resources in the node block being connected exist in the resource pool.

Resources:
['freesurfer-subject-dir', 'pipeline-fs_raw-average', 'pipeline-fs_subcortical-seg']

Screenshots / relevant information:

I am not seeing a resource pool in the default pipeline, so I am confused about where this error may be.

2

Hi, thank you for reaching out! If you are not running FreeSurfer or pulling in FreeSurfer outputs, the FreeSurfer tissue segmentation option won’t work. That option creates surface-derived tissue masks and relies on FreeSurfer outputs to do so.

3

Thanks. Is there a section in the pipeline where I can specify that I want to run FreeSurfer?

4

Yes, if you wish to run FreeSurfer you can toggle it in the surface_analysis section. Turn on abcd_prefreesurfer_prep and run_reconall, and if you wish to run post-FreeSurfer you can turn that on here as well.

If you have precomputed FreeSurfer outputs, you can turn on ingress_reconall and follow these instructions to specify your FreeSurfer output directory in the data config.

surface_analysis:

  # Run freesurfer_abcd_preproc to obtain preprocessed T1w for reconall
  abcd_prefreesurfer_prep:
    run: On

  # Will run Freesurfer for surface-based analysis. Will output traditional Freesurfer derivatives.
  # If you wish to employ Freesurfer outputs for brain masking or tissue segmentation in the voxel-based pipeline,
  # select those 'Freesurfer-' labeled options further below in anatomical_preproc.
  freesurfer:
    run_reconall: On

    # Ingress freesurfer recon-all folder
    ingress_reconall: Off

  # Run ABCD-HCP post FreeSurfer and fMRISurface pipeline
  post_freesurfer:
    run: On

Let me know if you have any trouble!

5

I am going to jump in here and ask how I can specify already processed FreeSurfer outputs into the connfig file.
Thanks.

6

Hi Joshua! You can follow these instructions. Basically, you just have to add a freesurfer_dir to the anat subsection of the data config for each subject you want to run. It should look like this:

- 
      anat:
        T1w: $PATH_TO/T1w.nii.gz
        freesurfer_dir: $PATH_TO/freesurfer/$SUBDIR/$SUBDIR
      func:
        func-run-1:
          scan: $PATH_TO/run-1_bold.nii.gz
          scan_parameters: $PATH_TO/run-1_bold.json
        func-run-2:
          scan: $PATH_TO/run-2_bold.nii.gz
          scan_parameters: $PATH_TO/run-2_bold.json
      site: $SITE
      subject_id: $SUB
      unique_id: $SES

Let me know if you have any issues with this!