Skip to content

🐛 abcd-options: missing space-bold_desc-brain_mask #2248

@shnizzedy

Description

@shnizzedy

Describe the bug

LookupError: When trying to connect node block 'nuisance_regressors_generation_T1w' to workflow 'cpac_pipeline_cpac_abcd-options_sub-NDARAB348EWR_ses-1' after node block 'erode_mask_boldWM': 

[!] C-PAC says: None of the listed resources are in the resource pool:

  'space-bold_desc-brain_mask' can be output from:
    bold_mask_afni (CPAC.func_preproc.func_preproc.bold_mask_afni)
    bold_mask_anatomical_based (CPAC.func_preproc.func_preproc.bold_mask_anatomical_based)
    bold_mask_anatomical_refined (CPAC.func_preproc.func_preproc.bold_mask_anatomical_refined)
    bold_mask_ccs (CPAC.func_preproc.func_preproc.bold_mask_ccs)
    bold_mask_fsl (CPAC.func_preproc.func_preproc.bold_mask_fsl)
    bold_mask_fsl_afni (CPAC.func_preproc.func_preproc.bold_mask_fsl_afni)
    distcor_blip_afni_qwarp (CPAC.distortion_correction.distortion_correction.distcor_blip_afni_qwarp)
    distcor_blip_fsl_topup (CPAC.distortion_correction.distortion_correction.distcor_blip_fsl_topup)
    func_mask_normalize (CPAC.func_preproc.func_preproc.func_mask_normalize)

Options:
- You can enable a node block earlier in the pipeline which produces these resources. Check the 'outputs:' field in a node block's documentation.
- You can directly provide this required data by pulling it from another BIDS directory using 'source_outputs_dir:' in the pipeline configuration, or by placing it directly in your C-PAC output directory.
- If you have done these, and you still get this message, please let us know through any of our support channels at: https://fcp-indi.github.io/
- ```

### To reproduce

I discovered it testing 2df6cb439ca74db9b6797713adae9adccf06097f (a2c3d2f10253083bf695b3d202b85a2acf93260b 🔀 #2230 🔀 #2241 🔀 #2246 🔀 #2247), but it's been in the smoke tests at least since #2215 was [merged into develop](https://github.com/FCP-INDI/C-PAC/actions/runs/15640548880/job/44067249927)

### Preconfig

- [x] abcd-options

### Run command

```BASH
singularity run \
  --cleanenv \
  -B "$OUTPUT":"$OUTPUT" \
  "$IMAGE" \
  "$INPUT" \
  "$OUTPUT" \
  participant \
  --skip_bids_validator \
  --n_cpus 1 \
  --mem_gb 7.0 \
  --participant_label "$PARTICIPANT" \
  --preconfig "$CONFIG_NAME"

Expected behavior

All preconfigs can connect and run.

Acceptance criteria

  • space-bold_desc-brain_mask is available for nuisance_regressors_generation_T1w,
    or
  • space-bold_desc-brain_mask is not needed for abcd-options preconfig

C-PAC version

v1.8.8-dev @ 2df6cb4

Container platform

Apptainer

Docker and/or Singularity version(s)

Apptainer v1.4.1-1.el8

Metadata

Metadata

Assignees

No one assigned

    Type

    Projects

    Status

    ✅ Done

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions