Run time error

[colon-perez]

Hello,

I have this error popping up. I was hoping to see if anyone has run into the same problem. I am trying to figure the best settings for my data. I am using the SIGMA atlas and I was able to run one time with the suggested settings but then I try to run the following command.

docker run -it --rm --platform linux/amd64 \
-v $PWD/Naive:/input_BIDS:ro \
-v $PWD/preprocess_outputs:/preprocess_outputs/ \ 
-v /Users/lmc0409/Documents/SIGMA_Wistar_Rat_Brain_TemplatesAndAtlases_Version1.2.1/SIGMA_Rat_Anatomical_Imaging/SIGMA_Rat_Anatomical_InVivo_Template/:/SIGMA/ \
-v /Users/lmc0409/Documents/SIGMA_Wistar_Rat_Brain_TemplatesAndAtlases_Version1.2.1/SIGMA_Rat_Brain_Atlases/SIGMA_Anatomical_Atlas/InVivo_Atlas/:/Atlas/ \
gabdesgreg/rabies:0.4.8 -p MultiProc preprocess /input_BIDS/ /preprocess_outputs/ --apply_STC --TR 4.0 --commonspace_reg masking=true,brain_extraction=false,template_registration=SyN,fast_commonspace=false --bold_robust_inho_cor apply=true,masking=false,brain_extraction=false,template_registration=SyN --anat_template=/SIGMA/SIGMA_InVivo_Brain_Template.nii --brain_mask=/SIGMA/SIGMA_InVivo_Brain_Mask.nii --WM_mask=/SIGMA/SIGMA_InVivo_WM_mask.nii --CSF_mask=/SIGMA/SIGMA_InVivo_CSF_mask2.nii --vascular_mask=/SIGMA/SIGMA_InVivo_Brain_Mask.nii --labels=/Atlas/SIGMA_InVivo_Anatomical_Brain_Atlas.nii

Then I get the following error. I also uploaded the log file just in case

***********************************
230907-21:47:38,318 nipype.workflow ERROR:
    could not run node: main_wf.anat_inho_cor_wf.InhoCorrection.a1
230907-21:47:38,324 nipype.workflow INFO:
    crashfile: /home/rabies/crash-20230907-213321-rabies-InhoCorrection.a1-7b8e0e7b-5828-471d-bf01-66fc3db688e0.pklz
230907-21:47:38,331 nipype.workflow INFO:
    ***********************************
230907-21:47:38,335 nipype.workflow CRITICAL:
    RABIES failed: Workflow did not execute cleanly. Check log for details
Traceback (most recent call last):
 File "/home/rabies/miniforge/bin/rabies", line 7, in <module>
   exec(compile(f.read(), __file__, 'exec'))
 File "/home/rabies/RABIES/scripts/rabies", line 3, in <module>
   execute_workflow()
 File "/home/rabies/RABIES/rabies/run_main.py", line 57, in execute_workflow
   graph_out = workflow.run(plugin=opts.plugin, plugin_args={'max_jobs': 50, 'dont_resubmit_completed_jobs': True,
 File "/home/rabies/miniforge/lib/python3.9/site-packages/nipype/pipeline/engine/workflows.py", line 632, in run
   runner.run(execgraph, updatehash=updatehash, config=self.config)
 File "/home/rabies/miniforge/lib/python3.9/site-packages/nipype/pipeline/plugins/base.py", line 192, in run
   report_nodes_not_run(notrun)
 File "/home/rabies/miniforge/lib/python3.9/site-packages/nipype/pipeline/plugins/tools.py", line 97, in report_nodes_not_run
   raise RuntimeError(
RuntimeError: Workflow did not execute cleanly. Check log for details

rabies_preprocess.log

[Gab-D-G]

Hi, I am not sure what happened, but I suspect a memory error as the registration was killed:

/home/rabies/miniforge/bin/antsRegistration_affine_SyN.sh: line 530: 34437 Killed                  antsRegistration --dimensionality 3 ${_arg_verbose} ${minc_mode} ${_arg_float} --output [ ${_arg_outputbasename} ] --use-histogram-matching ${_arg_histogram_matching} --initial-moving-transform "${second_stage_initial}" --transform SyN[ ${_arg_syn_control} ] ${syn_metric} $(eval echo ${steps_syn}) --masks [ ${fixedmask},${movingmask} ]
Failed at 522: antsRegistration --dimensionality 3 ${_arg_verbose} ${minc_mode} ${_arg_float} --output [ ${_arg_outputbasename} ] --use-histogram-matching ${_arg_histogram_matching} --initial-moving-transform "${second_stage_initial}" --transform SyN[ ${_arg_syn_control} ] ${syn_metric} $(eval echo ${steps_syn}) --masks [ ${fixedmask},${movingmask} ]

Perhaps your system was overloaded when running in parallel (whereas it was working if running with a single thread), I suggest lowering the number of threads with --local_threads or modulating the --scale_min_memory parameters.

[colon-perez]

It looks good to me. One of these pictures is the qc report image and the other is the file requested opened in fsleyes.

[colon-perez]

Actually the QC report for its for the second dataset (number 23) where as 22 is not there, so it stops prior generating anat inho qc report for subject 22

[Gab-D-G]

So there are actually two different errors in your log: 1) the inho QC report was not generated for subject 22, and 2) the template generation stage fails. I just noticed now that during the template generation stage there is the following error which is raised when trying to register the subject 22: Description: itk::ERROR: ITK only supports orthonormal direction cosines. No orthonormal definition found!. That's the original issue. Orthonormal direction can't be processed by various functions, so this needs to be corrected. A manual solution was discussed in this issue #160, otherwise the latest version of RABIES (0.5.1) now has a built-in correction with --oblique2card. You can correct this issue and then it should run appropriately!

[colon-perez]

After answering your questions and seeing the files were ok, I thought something may be wrong with the bold itself registering to T2. I am now testing this; if it fails, I'll look into the latest version of rabies. A while ago, I had an issue with the M1 processor, and the recommendation was to go with 4.8, but one of my students has 5.1 on an M2, and it seems to be fine. Different processor but I hope it will be ok. I will share my findings in case someone in the future runs into a similar issue.

[colon-perez]

I believe 5.1 is fixed. Now it's gone through more than before and the commonspace reg is completed for at least one. Appreciate the help.