qsiprep: Gradients or original files don't match

Hi @mattcieslak,

I got the following crash report when running qsiprep 0.14.2 for dsi data collected with two runs and a fieldmap:

Node: qsiprep_wf.single_subject_BR371_wf.dwi_preproc_ses_1_dir_AP_wf.confounds_wf.concat Working directory: /tmp/work/qsiprep_wf/single_subject_BR371_wf/dwi_preproc_ses_1_dir_AP_wf/confounds_wf/concat

Node inputs:

denoising_confounds = /tmp/work/qsiprep_wf/single_subject_BR371_wf/dwi_preproc_ses_1_dir_AP_wf/pre_hmc_wf/merge_and_denoise_wf/merge_dwis/dwi_denoise_ses_1_dir_AP__merged_confounds.csv fd = /tmp/work/qsiprep_wf/single_subject_BR371_wf/dwi_preproc_ses_1_dir_AP_wf/confounds_wf/fdisp/fd_power_2012.txt motion = /tmp/work/qsiprep_wf/single_subject_BR371_wf/dwi_preproc_ses_1_dir_AP_wf/confounds_wf/add_motion_headers/eddy_correctedspm_rp_motion.tsv original_bvals = [‘/tmp/work/qsiprep_wf/single_subject_BR371_wf/dwi_preproc_ses_1_dir_AP_wf/pre_hmc_wf/merge_and_denoise_wf/merge_dwis/dwi_denoise_ses_1_dir_AP__merged.bval’] original_bvecs = [‘/tmp/work/qsiprep_wf/single_subject_BR371_wf/dwi_preproc_ses_1_dir_AP_wf/pre_hmc_wf/merge_and_denoise_wf/merge_dwis/dwi_denoise_ses_1_dir_AP__merged.bvec’] original_files = [‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-1_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’, ‘/data/sub-BR371/ses-1/dwi/sub-BR371_ses-1_dir-AP_run-2_dwi.nii.gz’] sliceqc_file = /tmp/work/qsiprep_wf/single_subject_BR371_wf/dwi_preproc_ses_1_dir_AP_wf/hmc_sdc_wf/eddy/eddy_corrected.eddy_outlier_n_sqr_stdev_map

Traceback (most recent call last): File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py”, line 344, in _send_procs_to_workers self.procs[jobid].run(updatehash=updatehash) File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 516, in run result = self._run_interface(execute=True) File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 635, in _run_interface return self._run_command(execute) File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 741, in _run_command result = self._interface.run(cwd=outdir) File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 428, in run runtime = self._run_interface(runtime) File “/usr/local/miniconda/lib/python3.7/site-packages/qsiprep/interfaces/confounds.py”, line 61, in _run_interface newpath=runtime.cwd, File “/usr/local/miniconda/lib/python3.7/site-packages/qsiprep/interfaces/confounds.py”, line 171, in _gather_confounds raise Exception(“Gradients or original files don’t match. File a bug report!”) Exception: Gradients or original files don’t match. File a bug report!

This is the command I used to run qsiprep: #Run qsiprep qsiprep-docker $bids_root_dir $bids_root_dir/derivatives \ participant \ --participant-label $subj \ --skip_bids_validation \ --fs-license-file $HOME/BRAINY_BIDS/derivatives/license.txt \ --output-resolution 1.2 \ --nthreads $nthreads \ --stop-on-first-crash \ --mem_mb $mem_mb

Please let me know your thoughts on how best to proceed, thank you!