fMRIPrep error for subject: "_desc_preproc_wf.bold_reg_wf.fsl_bbr_wf.compare_transforms"


I am re-running all of my fMRIPrep preprocessing with a different template to resample to, using “–output-spaces MNI152NLin6Asym:res-2” rather than the standard 2009c fMRIPrep template. All of my preprocessing with fMRIPrep have run successfully except for one subject. This subject was fine when preprocessing with 2009c template. My initial issue with this participant while re-running pre-processing was that there was a memory error. Per a recommendation on another Neurostars post, I then added the command, “–skip_bids_validation”. Command looks like this:

singularity run --cleanenv -B /home/ /home/my_images/fmriprep-1.4.0.simg
Feedback/feedback_BIDS/ /home/Feedback/feedback_BIDS/derivatives/
participant --participant_label 05 --fs-license-file Feedback/feedback_BIDS/code/license.txt
–nthreads 16 --omp-nthreads 16 --fs-no-reconall --fd-spike-threshold 0.6 --output-spaces MNI152NLin6Asym:res-2 --skip_bids_validation
-w Feedback/feedback_BIDS/derivatives/scratch/ >> Feedback/preprocess/fMRIPrepCommandOutput/sub05.txt &

After doing skip bids validation, it runs for hours and it appears to be nearly finished (everything appears to be output in derivatives and most of the output you’d expect is in scratch directory) but eventually it crashes with the following Errors reported in html:

fMRIPrep failed: Workflow did not execute cleanly. Check log for details

Preprocessing did not finish successfully. Errors occurred while processing data from participants: 05 (6). Check the HTML reports for details.


  • Node Name: fmriprep_wf.single_subject_05_wf.func_preproc_task_feedback_run_6_space_MNI152NLin2009cAsym_desc_preproc_wf.bold_reg_wf.fsl_bbr_wf.compare_transforms

  • Node Name: fmriprep_wf.single_subject_05_wf.func_preproc_task_feedback_run_5_space_MNI152NLin2009cAsym_desc_preproc_wf.bold_reg_wf.fsl_bbr_wf.compare_transforms

  • Node Name: fmriprep_wf.single_subject_05_wf.func_preproc_task_feedback_run_1_space_MNI152NLin2009cAsym_desc_preproc_wf.bold_reg_wf.fsl_bbr_wf.compare_transforms

  • Node Name: fmriprep_wf.single_subject_05_wf.func_preproc_task_feedback_run_2_space_MNI152NLin2009cAsym_desc_preproc_wf.bold_reg_wf.fsl_bbr_wf.compare_transforms

  • Node Name: fmriprep_wf.single_subject_05_wf.func_preproc_task_feedback_run_4_space_MNI152NLin2009cAsym_desc_preproc_wf.bold_reg_wf.fsl_bbr_wf.compare_transforms

  • Node Name: fmriprep_wf.single_subject_05_wf.func_preproc_task_feedback_run_3_space_MNI152NLin2009cAsym_desc_preproc_wf.bold_reg_wf.fsl_bbr_wf.compare_transforms

I’ve re-run this a few times, double-checked if it’s BIDS validated, if there any issues with the data itself, etc. but it all looks good to me.

Does anyone have any sense for what may be occurring here? I can’t figure it out. I’m particularly confused since both this memory error and the error related to compare_transforms did not occur when I was doing this on the first try, resampling to 2009c rather than MNI152NLin6Asym:res-2.

Any help would be greatly appreciated!

Hello, if anyone encounters a related issue, I resolved it by following what this person did. They had a similar issue and set the working space to the temporary directory with “-w $TMPDIR” and then I finally didn’t get these issues described above.