bvec/bval files with suffix like "run-1" and "run-2" do not combine

[weiwei-wch]

Summary

Hi, recently I tried the newest version of qsiprep (1.0.0rc2), I meet several problems:

1. the data in different acq do not merge as one file like in the old version (0.22.0), this prolem is like Add option to revert to old behaviour of grouping scans across different acquisitions? #897, I try to add MultipartID in the json file, while nothing have changed, is this implemented?
2. the data in different run, like run-1 and run-2, do not merge and cause an error, which seems caused by the unmerged bvec/bval file.
3. the SDC was not performed, even I have both PA and AP phase encoding file, I tried remove one run of PA data, but the SDC still not happen.

the BIDS structure is like follow:

sub-N0016F00nLHX_ses-0W_acq-b0d6_dir-PA_run-1_dwi.bval
sub-N0016F00nLHX_ses-0W_acq-b0d6_dir-PA_run-1_dwi.bvec
sub-N0016F00nLHX_ses-0W_acq-b0d6_dir-PA_run-1_dwi.json
sub-N0016F00nLHX_ses-0W_acq-b0d6_dir-PA_run-1_dwi.nii.gz
sub-N0016F00nLHX_ses-0W_acq-b0d6_dir-PA_run-2_dwi.bval
sub-N0016F00nLHX_ses-0W_acq-b0d6_dir-PA_run-2_dwi.bvec
sub-N0016F00nLHX_ses-0W_acq-b0d6_dir-PA_run-2_dwi.json
sub-N0016F00nLHX_ses-0W_acq-b0d6_dir-PA_run-2_dwi.nii.gz
sub-N0016F00nLHX_ses-0W_acq-b1000d32_dir-AP_dwi.bval
sub-N0016F00nLHX_ses-0W_acq-b1000d32_dir-AP_dwi.bvec
sub-N0016F00nLHX_ses-0W_acq-b1000d32_dir-AP_dwi.json
sub-N0016F00nLHX_ses-0W_acq-b1000d32_dir-AP_dwi.nii.gz
sub-N0016F00nLHX_ses-0W_acq-b2000d32_dir-AP_dwi.bval
sub-N0016F00nLHX_ses-0W_acq-b2000d32_dir-AP_dwi.bvec
sub-N0016F00nLHX_ses-0W_acq-b2000d32_dir-AP_dwi.json
sub-N0016F00nLHX_ses-0W_acq-b2000d32_dir-AP_dwi.nii.gz
sub-N0016F00nLHX_ses-0W_acq-b3000d32_dir-AP_run-1_dwi.bval
sub-N0016F00nLHX_ses-0W_acq-b3000d32_dir-AP_run-1_dwi.bvec
sub-N0016F00nLHX_ses-0W_acq-b3000d32_dir-AP_run-1_dwi.json
sub-N0016F00nLHX_ses-0W_acq-b3000d32_dir-AP_run-1_dwi.nii.gz
sub-N0016F00nLHX_ses-0W_acq-b3000d32_dir-AP_run-2_dwi.bval
sub-N0016F00nLHX_ses-0W_acq-b3000d32_dir-AP_run-2_dwi.bvec
sub-N0016F00nLHX_ses-0W_acq-b3000d32_dir-AP_run-2_dwi.json
sub-N0016F00nLHX_ses-0W_acq-b3000d32_dir-AP_run-2_dwi.nii.gz

The results I get are seperated for each acq, and those data with run-1 and run-2 are not excuted in results and here is the error details in the report file:

File: <workdir>/sub-ADP0001F00nTJY/log/20241213-040009_81f8aa0a-634b-41e9-bba4-7f59128437d8/crash-20241213-041444-UID1005-raw_src-16e248c9-05dc-4df8-ab4b-c4258d0029b5.txt
Working Directory: /work/qsiprep_1_0_wf/sub_ADP0001F00nTJY_ses_0W_wf/dwi_preproc_ses_0W_acq_b0d6_dir_PA_wf/pre_hmc_wf/merge_and_denoise_wf/dwi_qc_wf/raw_src
Inputs:

    args:
    bvec_convention: FSL
    environ: {}
    grad_dev:
    input_b_table_file:
    input_bvals_file:
    input_bvecs_file:
    input_dicom_dir:
    input_nifti_file:
    num_threads: 1
    output_src:
    recursive:
    subject_id:
    test_trait:

Traceback (most recent call last):
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 66, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 525, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 643, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 769, in _run_command
    raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node raw_src.

Cmdline:
	dsi_studio --action=src  --bval=/work/qsiprep_1_0_wf/sub_ADP0001F00nTJY_ses_0W_wf/dwi_preproc_ses_0W_acq_b0d6_dir_PA_wf/pre_hmc_wf/merge_and_denoise_wf/merge_dwis/dwi_denoise_ses_0W_acq_b0d6_dir_PA__merged.bval --bvec=/work/qsiprep_1_0_wf/sub_ADP0001F00nTJY_ses_0W_wf/dwi_preproc_ses_0W_acq_b0d6_dir_PA_wf/pre_hmc_wf/merge_and_denoise_wf/merge_dwis/dwi_denoise_ses_0W_acq_b0d6_dir_PA__merged.bvec --source=/work/qsiprep_1_0_wf/sub_ADP0001F00nTJY_ses_0W_wf/dwi_preproc_ses_0W_acq_b0d6_dir_PA_wf/pre_hmc_wf/merge_and_denoise_wf/raw_merge/sub-ADP0001F00nTJY_ses-0W_acq-b0d6_dir-PA_run-1_dwi_merged.nii.gz --thread_count=1 --output=/work/qsiprep_1_0_wf/sub_ADP0001F00nTJY_ses_0W_wf/dwi_preproc_ses_0W_acq_b0d6_dir_PA_wf/pre_hmc_wf/merge_and_denoise_wf/dwi_qc_wf/raw_src/sub-ADP0001F00nTJY_ses-0W_acq-b0d6_dir-PA_run-1_dwi_merged.src.gz
Stdout:
	DSI Studio version: Hou "??" Aug  2 2024
	[1;34m??command line�[0m
	[0;32msource�[0m=/work/qsiprep_1_0_wf/sub_ADP0001F00nTJY_ses_0W_wf/dwi_preproc_ses_0W_acq_b0d6_dir_PA_wf/pre_hmc_wf/merge_and_denoise_wf/raw_merge/sub-ADP0001F00nTJY_ses-0W_acq-b0d6_dir-PA_run-1_dwi_merged.nii.gz
	[0;32maction�[0m=src
	[0;32mloop�[0m=/work/qsiprep_1_0_wf/sub_ADP0001F00nTJY_ses_0W_wf/dwi_preproc_ses_0W_acq_b0d6_dir_PA_wf/pre_hmc_wf/merge_and_denoise_wf/raw_merge/sub-ADP0001F00nTJY_ses-0W_acq-b0d6_dir-PA_run-1_dwi_merged.nii.gz
	1;34m??run src�[0m
	1;35m??opening sub-ADP0001F00nTJY_ses-0W_acq-b0d6_dir-PA_run-1_dwi_merged.nii�[0m
	convert 4D NIFTI to src
	576ms
	[0;32mbvec�[0m=/work/qsiprep_1_0_wf/sub_ADP0001F00nTJY_ses_0W_wf/dwi_preproc_ses_0W_acq_b0d6_dir_PA_wf/pre_hmc_wf/merge_and_denoise_wf/merge_dwis/dwi_denoise_ses_0W_acq_b0d6_dir_PA__merged.bvec
	bval�[0m=/work/qsiprep_1_0_wf/sub_ADP0001F00nTJY_ses_0W_wf/dwi_preproc_ses_0W_acq_b0d6_dir_PA_wf/pre_hmc_wf/merge_and_denoise_wf/merge_dwis/dwi_denoise_ses_0W_acq_b0d6_dir_PA__merged.bval
	cannot create SRC file: cannot find bval/bvec file�[0m
	580ms
	584ms
Stderr:

Traceback:
	RuntimeError: subprocess exited with code 1.