Getting Non-zero exit code with a success message

[RamoneAgard]

What happened?

fMRIPrep is running seemingly fine, and when it gets to the end of the program I receive the messages "fMRIPrep finished successfully!" and "Works derived from this fMRIPrep execution should include the boilerplate text found in <OUTPUT_PATH>/logs/CITATION.md.", but the exit code from fmriprep is 1. It appears that all of the output files are present and no crash files are created, but now I am wondering if there is a real error being missed, or if this is a bug. I am running this with apptainer, and even went inside the image with 'apptainer shell' to make sure it was the fmriprep binary that is giving the exit code.

What command did you use?

fmriprep /data /out participant --participant-label Sleep06 -w /work --verbose --fd-spike-threshold 0.9 --cifti-output 91k --output-spaces fsLR MNI152NLin6Asym:res-2 --stop-on-first-crash --nprocs 48 --random-seed 1234 --project-goodvoxels --medial-surface-nan

What version of fMRIPrep are you running?

25.2.5

How are you running fMRIPrep?

Singularity

Is your data BIDS valid?

Yes

Are you reusing any previously computed results?

No

Please copy and paste any relevant log output.

260324-19:45:50,849 nipype.workflow INFO:                                                                                                                                                                                                                             
         [Node] Outdated cache found for "fmriprep_25_2_wf.sub_Sleep06_ses_01_wf.bold_ses_01_task_rest_run_02_echo_1_wf.carpetplot_wf.ds_report_bold_conf".                                                                                                            
260324-19:45:50,851 nipype.workflow INFO:                                                                                                                                                                                                
         [Node] Setting-up "fmriprep_25_2_wf.sub_Sleep06_ses_01_wf.bold_ses_01_task_rest_run_02_echo_1_wf.carpetplot_wf.ds_report_bold_conf" in "/work/fmriprep_25_2_wf/sub_Sleep06_ses_01_wf/bold_ses_01_task_rest_run_02_echo_1_wf/carpetplot_wf/ds_report_bold_conf".
260324-19:45:50,853 nipype.workflow INFO:                                                                                                                                                                                    
         [Node] Outdated cache found for "fmriprep_25_2_wf.sub_Sleep06_ses_01_wf.bold_ses_01_task_rest_run_02_echo_1_wf.carpetplot_wf.ds_report_bold_conf".                                                                
260324-19:45:50,927 nipype.workflow INFO:                                                                                                                                                                                    
         [Node] Executing "ds_report_bold_conf" <fmriprep.interfaces.DerivativesDataSink>                                                                                                                                  
260324-19:45:51,79 nipype.workflow INFO:                                                                                                                                                                                     
         [Node] Finished "ds_report_bold_conf", elapsed time 0.145528s.                                                                                                                                                    
260324-19:45:51,161 nipype.workflow INFO:                                                                                                                                                                                    
         [Job 769] Completed (fmriprep_25_2_wf.sub_Sleep06_ses_01_wf.bold_ses_01_task_rest_run_02_echo_1_wf.carpetplot_wf.ds_report_bold_conf).                                                                            
260324-19:45:54,973 nipype.workflow INFO:                                                                                                                                                                                      
         [MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 443.89/453.01, Free processors: 47/48, Free GPU slot:0/0.                                                                                               
                     Currently running:                                                                                                                                                                                    
                       * fmriprep_25_2_wf.sub_Sleep06_ses_01_wf.bold_ses_01_task_rest_run_01_echo_1_wf.carpetplot_wf.conf_plot                                                                                                         
260324-19:46:28,675 nipype.workflow INFO:                                                                                                                                                                                                  
         [Node] Finished "conf_plot", elapsed time 209.95323s.                                                                                                                                                                                 
260324-19:46:31,539 nipype.workflow INFO:                                                                                                                                                                                                         
         [Job 765] Completed (fmriprep_25_2_wf.sub_Sleep06_ses_01_wf.bold_ses_01_task_rest_run_01_echo_1_wf.carpetplot_wf.conf_plot).                                                                                                               
260324-19:46:31,556 nipype.workflow INFO:                                                                                                                                                                                                              
         [MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 453.01/453.01, Free processors: 48/48, Free GPU slot:0/0.                                                                                                                        
260324-19:46:35,699 nipype.workflow INFO:                                                                                                                                                                                                                     
         [Node] Outdated cache found for "fmriprep_25_2_wf.sub_Sleep06_ses_01_wf.bold_ses_01_task_rest_run_01_echo_1_wf.carpetplot_wf.ds_report_bold_conf".                                                                                                     
260324-19:46:35,713 nipype.workflow INFO:                                                                                                                                                                                                                         
         [Node] Outdated cache found for "fmriprep_25_2_wf.sub_Sleep06_ses_01_wf.bold_ses_01_task_rest_run_01_echo_1_wf.carpetplot_wf.ds_report_bold_conf".                                                                                                           
260324-19:46:35,716 nipype.workflow INFO:                                                                                                                                                                                                                              
         [Node] Setting-up "fmriprep_25_2_wf.sub_Sleep06_ses_01_wf.bold_ses_01_task_rest_run_01_echo_1_wf.carpetplot_wf.ds_report_bold_conf" in "/work/fmriprep_25_2_wf/sub_Sleep06_ses_01_wf/bold_ses_01_task_rest_run_01_echo_1_wf/carpetplot_wf/ds_report_bold_conf".
260324-19:46:35,734 nipype.workflow INFO:                                                                                                                                                                                            
         [Node] Outdated cache found for "fmriprep_25_2_wf.sub_Sleep06_ses_01_wf.bold_ses_01_task_rest_run_01_echo_1_wf.carpetplot_wf.ds_report_bold_conf".                                                                              
260324-19:46:35,809 nipype.workflow INFO:                                                                                                                                                                                                    
         [Node] Executing "ds_report_bold_conf" <fmriprep.interfaces.DerivativesDataSink>                                                                                                                                  
260324-19:46:35,962 nipype.workflow INFO:                                                                                                                                                                                    
         [Node] Finished "ds_report_bold_conf", elapsed time 0.146325s.                                                                                                                                                          
260324-19:46:36,41 nipype.workflow INFO:                                                                                                                                                                                                                 
         [Job 768] Completed (fmriprep_25_2_wf.sub_Sleep06_ses_01_wf.bold_ses_01_task_rest_run_01_echo_1_wf.carpetplot_wf.ds_report_bold_conf).                                                                                      
260324-19:46:40,568 nipype.workflow IMPORTANT:                                                                                                                                                                                           
         fMRIPrep finished successfully!                                                                                                                                                                                                     
260324-19:46:40,627 nipype.workflow IMPORTANT:                                                                                                                                                                                                   
         Works derived from this fMRIPrep execution should include the boilerplate text found in <OUTPUT_PATH>/logs/CITATION.md.                                                                                                                    
Apptainer> echo $?                                                                                                                                                                                                                                    
1

Additional information / screenshots

No response

[mgxd]

if there are no hidden errors buried in the log, it's probably an error raised after the workflow has completed (this can be improved..)- is there anything visually off with the reports?

[RamoneAgard]

The T2* maps look a little 'stripy' but there are no error messages in any of the stdout text.

[RamoneAgard]

I was able to find the cause of the T2* maps looking different (was an issue with my data), but it seems like the only potential error occurring is in the carpetplots/grayplots. It looks like something could be going wrong in the sampling of the "Edge" vertices/voxels where chunks of grey 'blank' patches are in the plot, but I'm not sure if I am just seeing consecutive rows of voxels with "zero" data.