Executive summary is not generated when running anat-only

What happened?

When processing anat-only with the --ignore func flag, the pipeline fails to create executive summary outputs. When executive summary is called, it points to the func dir for bids-input and as a result does not make the summary_DCANBOLDProc_v4.0.0 folder:

running ExecutiveSummary
/opt/dcan-tools/executivesummary/ExecutiveSummary.py \
    --bids-input=/bids_dir/sub-<id>/ses-<id>/func \
    --output-dir=/output_dir/sub-<id>/ses-<id>/files \
    --participant-label=<id>\
    --session-id=<id> \
    --atlas=/opt/pipeline/global/templates/MNI152_T1_1mm_brain.nii.gz \
    --dcan-summary=summary_DCANBOLDProc_v4.0.0

This can be resolved by setting --dcan-summary in this call to None if running anat-only (similar to the infant pipeline)

@tpandhi has made these updates in PR 121 that includes other changes that we'll want to review separately

What command did you use?

env -i ${singualrity} run \
-B ${data_dir}/bids_dataset:/bids_dir \
-B ${data_dir}/derivatives/abcd-hcp-pipeline_v0.1.4:/output_dir \
-B ${run_dir}/license.txt:/opt/freesurfer/license.txt \
-B ${run_dir}/ABCD_BIDS_cleaning.json:/ABCD_BIDS_cleaning.json \
-B /path/to/updated/run.py:/app/run.py \
-B /path/to/updated/pipelines.py:/app/pipelines.py \
/home/faird/shared/code/internal/pipelines/ABCD-BIDS/abcd-hcp-pipeline_R2019a-test_07222024a.sif \
/bids_dir /output_dir \
--freesurfer-license /opt/freesurfer/license.txt \
--participant-label ${subject_id} \
--custom-clean /ABCD_BIDS_cleaning.json \
--ignore func \
--stage ExecutiveSummary \
--ncpus 8

What version of the abcd-hcp pipeline are you using?

v0.1.4

Directory Structure

No response

Relevant log output

From Exec Summ pipeline logs:

Directory does not exist: /output_dir/sub-<id>/ses-<id>/files/summary_DCANBOLDProc_v4.0.0
Exiting.

Add any additional information or context about the problem here.

No response

DCAN-Labs / abcd-hcp-pipeline