prep_segs_for_greedy error on Mac

[EmilySNichols]

Hi folks,

I'm attempting to run hippunfold on a new infant dataset, but am receiving an error I can't seem to fix. I'm using the Docker container on a Mac.

Here's what I'm running:
docker run -it --rm -v /Users/emilynichols/Documents/Comet:/bids -v /Users/emilynichols/Documents/Comet/derivatives/hippunfold:/output khanlab/hippunfold:latest /bids /output participant --participant_label Comet044 --modality T1w --force-nnunet-model neonateT1w_v2 --template dHCP --keep_work --cores all

It starts running, and things seem to be going well. The output directly before the error is:

[Mon Jan 20 18:31:46 2025]
Finished job 25.
35 of 274 steps (13%) done
Select jobs to execute...

[Mon Jan 20 18:31:46 2025]
rule prep_segs_for_greedy:
input: work/sub-Comet044/anat/sub-Comet044_hemi-L_space-template_desc-hipptissue_dseg.nii.gz
output: work/sub-Comet044/anat/sub-Comet044_hemi-L_space-template_desc-hipptissue_dsegsplit
jobid: 28
reason: Missing output files: work/sub-Comet044/anat/sub-Comet044_hemi-L_space-template_desc-hipptissue_dsegsplit; Input files updated by another job: work/sub-Comet044/anat/sub-Comet044_hemi-L_space-template_desc-hipptissue_dseg.nii.gz
wildcards: prefix=work/sub-Comet044/anat/sub-Comet044_hemi-L_space-template_desc-hipptissue
resources: tmpdir=/tmp

HTTP request sent, awaiting response... 301 MOVED PERMANENTLY
Location: /records/8209029/files/trained_model.3d_fullres.Task301_dhcp_T1w_synthseg_manuallycorrected.nnUNetTrainer.model_best.tar [following]
--2025-01-20 18:31:47-- https://zenodo.org/records/8209029/files/trained_model.3d_fullres.Task301_dhcp_T1w_synthseg_manuallycorrected.nnUNetTrainer.model_best.tar
Reusing existing connection to zenodo.org:443.
HTTP request sent, awaiting response... 200 OK
Length: 4901171200 (4.6G) [application/octet-stream]
Saving to: ‘/root/.cache/hippunfold/model/trained_model.3d_fullres.Task301_dhcp_T1w_synthseg_manuallycorrected.nnUNetTrainer.model_best.tar’

nthseg_manuallycorrected.nnUNetT 3%[=> ] 175.57M 6.15MB/s eta 8m 42s /bin/bash: line 1: 232 Killed c3d work/sub-Comet044/anat/sub-Comet044_hemi-L_space-template_desc-hipptissue_dseg.nii.gz -retain-labels 1 2 3 4 5 6 8 -split -foreach -smooth 0.5x0.5x0.5mm -endfor -oo work/sub-Comet044/anat/sub-Comet044_hemi-L_space-template_desc-hipptissue_dsegsplit/label_%02d.nii.gz
thseg_manuallycorrected.nnUNetTr 3%[=> ] 178.02M 6.26MB/s eta 8m 42s [Mon Jan 20 18:32:08 2025]

But then it throws the error:

Error in rule prep_segs_for_greedy:
jobid: 28
input: work/sub-Comet044/anat/sub-Comet044_hemi-L_space-template_desc-hipptissue_dseg.nii.gz
output: work/sub-Comet044/anat/sub-Comet044_hemi-L_space-template_desc-hipptissue_dsegsplit
shell:
mkdir -p work/sub-Comet044/anat/sub-Comet044_hemi-L_space-template_desc-hipptissue_dsegsplit && c3d work/sub-Comet044/anat/sub-Comet044_hemi-L_space-template_desc-hipptissue_dseg.nii.gz -retain-labels 1 2 3 4 5 6 8 -split -foreach -smooth 0.5x0.5x0.5mm -endfor -oo work/sub-Comet044/anat/sub-Comet044_hemi-L_space-template_desc-hipptissue_dsegsplit/label_%02d.nii.gz
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Removing output files of failed job prep_segs_for_greedy since they might be corrupted:
work/sub-Comet044/anat/sub-Comet044_hemi-L_space-template_desc-hipptissue_dsegsplit
tTrainer.model_best.tar 18%[===============> ] 887.39M 7.95MB/s eta 7m 31s [Mon Jan 20 18:33:33 2025]
Finished job 16.
36 of 274 steps (13%) done
/root/.cache/hippunfold/model/trained_mod 100%[=====================================================================================>] 4.56G 6.16MB/s in 10m 48s

2025-01-20 18:42:35 (7.21 MB/s) - ‘/root/.cache/hippunfold/model/trained_model.3d_fullres.Task301_dhcp_T1w_synthseg_manuallycorrected.nnUNetTrainer.model_best.tar’ saved [4901171200/4901171200]

[Mon Jan 20 18:42:35 2025]
Finished job 22.
37 of 274 steps (14%) done
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2025-01-20T183138.015911.snakemake.log

Any idea what this error means, and how to fix it?

Thanks!
Emily