🐛 `At least 2 warped image/label pairs needs to exist for jointFusion`

[shnizzedy]

Describe the bug

-------------------------------------------------------------------------------------- 
Start JLFization 
-------------------------------------------------------------------------------------- 

-------------------------------------------------------------------------------------- 
Parameters 
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ANTSPATH is /usr/lib/ants 

Dimensionality:           3 
Output prefix:            ants_multiatlas_ 
Posteriors format:         
Target image:             /p/himmelbach/fmolla/phd/CrossSpeciesConnectivity/cpac_runs_monkey_1core/default/working/cpac_sub-1001_ses-1/brain_extraction_58/sub-1001_T1w_resample_warp_noise_corrected_corrected_calc.nii.gz 
Atlas images:             s3://fcp-indi/resources/cpac/resources/MacaqueYerkes19_T1w_0.5mm/T1w_brain.nii.gz s3://fcp-indi/resources/cpac/resources/J_Macaque_11mo_atlas_nACQ_194x252x160space_0.5mm/T1w_brain.nii.gz 
Atlas labels:             s3://fcp-indi/resources/cpac/resources/MacaqueYerkes19_T1w_0.5mm/Segmentation.nii.gz s3://fcp-indi/resources/cpac/resources/J_Macaque_11mo_atlas_nACQ_194x252x160space_0.5mm/Segmentation.nii.gz 
Transformation:           b 

Keep all images:          0 
Processing type:          0 
Number of cpu cores:      2 
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./job_T1w_brain_0.sh 
./job_T1w_brain_1.sh 

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Starting JLF 
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ants_multiatlas_T1w_brain_0_Warped.nii.gz 
ants_multiatlas_T1w_brain_1_Warped.nii.gz 
Error:  At least 2 warped image/label pairs needs to exist for jointFusion. 

To reproduce

Run with --pipeline_file monkey_pip_diffmag_flag.yml

The specific command that crashes is

${ANTSPATH}${ANTSPATH:+/}antsJointLabelFusion.sh -d 3 -o ants_multiatlas_ -t /p/himmelbach/fmolla/phd/CrossSpeciesConnectivity/cpac_runs_monkey_1core/default/working/cpac_sub-1001_ses-1/brain_extraction_58/sub-1001_T1w_resample_warp_noise_corrected_corrected_calc.nii.gz -x /p/himmelbach/fmolla/phd/CrossSpeciesConnectivity/cpac_runs_monkey_1core/default/working/cpac_sub-1001_ses-1/refined_mask_53/MacaqueYerkes19_T1w_1_maths_trans_flirt_thresh.nii.gz -y b -c 0 -g s3://fcp-indi/resources/cpac/resources/MacaqueYerkes19_T1w_0.5mm/T1w_brain.nii.gz -l s3://fcp-indi/resources/cpac/resources/MacaqueYerkes19_T1w_0.5mm/Segmentation.nii.gz -g s3://fcp-indi/resources/cpac/resources/J_Macaque_11mo_atlas_nACQ_194x252x160space_0.5mm/T1w_brain.nii.gz -l s3://fcp-indi/resources/cpac/resources/J_Macaque_11mo_atlas_nACQ_194x252x160space_0.5mm/Segmentation.nii.gz

Expected behavior

Pipeline does not crash

Acceptance criteria

• [ ] pipeline does not crash

Screenshots

No response

C-PAC version

v1.8.2

Container platform

Singularity

Docker and/or Singularity version(s)

No response

Additional context

• cpax_forum Google Group: nhp-macaque pipeline where this issue was discovered
• Full C-PAC crashfile

[shnizzedy]

We should probably also beef up the C-PAC JLF docs and link to Multi-Atlas Segmentation with Joint Label Fusion