Error: Meld_graph script: run_script_segmentation.py

[farah-naz01]

Hi,
I am trying meld_graph in a docker container. Since I had already run the Fastsurfer, so I copied the Fastsurfer output in the meld-graph output folder. After running the command:

"docker-compose run meld_graph python scripts/new_patient_pipeline/new_pt_pipeline.py -harmo_code H120 -ids list_subjects.txt -demos /data/demographics_file_H120.csv --parallelise --fastsurfer --harmo_only"

I encountered this error.

Terminal Output:

STEP 1 - test017: Fastsurfer outputs already exists for subject test017. Freesurfer will be skipped
STEP 1 - test018: Fastsurfer outputs already exists for subject test018. Freesurfer will be skipped
STEP 1 - test012: Fastsurfer outputs already exists for subject test012. Freesurfer will be skipped
STEP 1 - test009: Fastsurfer outputs already exists for subject test009. Freesurfer will be skipped
STEP 1 - test019: Fastsurfer outputs already exists for subject test019. Freesurfer will be skipped
STEP 1 - test020: Fastsurfer outputs already exists for subject test020. Freesurfer will be skipped
Traceback (most recent call last):
File "/app/scripts/new_patient_pipeline/new_pt_pipeline.py", line 144, in
result = run_script_segmentation(
File "/app/scripts/new_patient_pipeline/run_script_segmentation.py", line 393, in run_script_segmentation
subject_ids_succeed = run_subjects_segmentation_parallel(subject_ids, harmo_code = harmo_code, use_fastsurfer = use_fastsurfer, verbose=verbose)
File "/app/scripts/new_patient_pipeline/run_script_segmentation.py", line 268, in run_subjects_segmentation_parallel
subjects_dict = subjects_dict[mask]
TypeError: list indices must be integers or slices, not list
ERROR: 1

(I saw the script: run_script_segmentation.py and the line "subjects_dict = subjects_dict[mask]" causing the error. I am not sure how to resolve it.)

Any help or guidance is appreciated.
Thanks!