Request for help with qsiprep run

[nadluru]

Dear qsiprep team,

We have been trying to run qsiprep on an example. We used the following steps. Currently I am not to share the exact dataset publicly but would appreciate any insights or hypotheses based on the error message. I can share the example dataset on a one-on-one basis but just not post it here publicly.

mkdir -p example_derivatives_qsiprep

docker run -ti --rm \
-v example:/input \
-v example_derivatives_qsiprep:/output \
-v ${FREESURFER_HOME}/license.txt:/input/license.txt \
-v /tmp:/workdir \
pennlinc/qsiprep:latest \
/input /output participant \
--omp-nthreads 1 \
--output-resolution 1.5 \
--skip-bids-validation \
--denoise-method dwidenoise \
--unringing-method mrdegibbs \
--hmc-model eddy \
--intramodal-template-transform BSplineSyN \
--stop-on-first-crash \
--write-graph \
--resource-monitor \
--work-dir workdir \
--anat-modality none \
--fs-license-file /input/license.txt`

It gives the message pasted below. Could you kindly look into this and guide us on how we could resolve this?

Thank you so much for your kind consideration and help.

Sincerely,
Nagesh

250312-02:02:05,925 nipype.workflow IMPORTANT:
         Running QSIPrep version 1.0.0rc2.dev0+g789be41.d20241119

         License NOTICE ##################################################
         QSIPrep 1.0.0rc2.dev0+g789be41.d20241119
         Copyright The PennLINC Developers.
         
         This product includes software developed by
         the NiPreps Community (https://nipreps.org/).
         
         Portions of this software were developed at the Department of
         Psychology at Stanford University, Stanford, CA, US.
         
         This software is also distributed as a Docker container image.
         The bootstrapping file for the image ("Dockerfile") is licensed
         under the MIT License.
         
         This software may be distributed through an add-on package called
         "Docker Wrapper" that is under the BSD 3-clause License.
         #################################################################
250312-02:02:05,937 nipype.workflow IMPORTANT:
         Building QSIPrep's workflow:
           * BIDS dataset path: /input.
           * Participant list: ['0003x203004544'].
           * Run identifier: 20250312-020154_0b5ed76f-a9fb-4b53-8c3b-5a9d0f770bac.
250312-02:02:05,988 nipype.workflow INFO:
         No anatomical scans will be processed! Visual reports will show template masks.
250312-02:02:05,996 nipype.workflow INFO:
         Combining all DWI files within each available session and acquisition:
250312-02:02:05,997 nipype.workflow INFO:
                - 2 scans in session 0001x2017x03x02/acquisition AxialxDTI
250312-02:02:06,14 nipype.workflow INFO:
         [{'dwi_series': ['/input/sub-0003x203004544/ses-0001x2017x03x02/dwi/sub-0003x203004544_ses-0001x2017x03x02_acq-AxialxDTI_dir-AP_dwi.nii.gz'], 'fieldmap_info': {'suffix': None}, 'dwi_series_pedir': '', 'concatenated_bids_name': 'sub-0003x203004544_ses-0001x2017x03x02_acq-AxialxDTI_dir-AP'}, {'dwi_series': ['/input/sub-0003x203004544/ses-0001x2017x03x02/dwi/sub-0003x203004544_ses-0001x2017x03x02_acq-AxialxDTI_dir-PA_dwi.nii.gz'], 'fieldmap_info': {'suffix': None}, 'dwi_series_pedir': '', 'concatenated_bids_name': 'sub-0003x203004544_ses-0001x2017x03x02_acq-AxialxDTI_dir-PA'}]
Process Process-2:
Traceback (most recent call last):
  File "/opt/conda/envs/qsiprep/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap
    self.run()
  File "/opt/conda/envs/qsiprep/lib/python3.10/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/cli/workflow.py", line 117, in build_workflow
    retval["workflow"] = init_qsiprep_wf()
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/workflows/base.py", line 83, in init_qsiprep_wf
    single_subject_wf = init_single_subject_wf(subject_id, session_ids)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/workflows/base.py", line 401, in init_single_subject_wf
    dwi_preproc_wf = init_dwi_preproc_wf(
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/workflows/dwi/base.py", line 247, in init_dwi_preproc_wf
    pre_hmc_wf = init_dwi_pre_hmc_wf(
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/workflows/dwi/pre_hmc.py", line 238, in init_dwi_pre_hmc_wf
    merge_dwis = init_merge_and_denoise_wf(
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/workflows/dwi/merge.py", line 151, in init_merge_and_denoise_wf
    dwi_df = get_acq_parameters_df(raw_dwi_files, layout=layout)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/workflows/dwi/merge.py", line 707, in get_acq_parameters_df
    ].str.replace("-", "")
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pandas/core/generic.py", line 5902, in __getattr__
    return object.__getattribute__(self, name)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pandas/core/accessor.py", line 182, in __get__
    accessor_obj = self._accessor(obj)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pandas/core/strings/accessor.py", line 181, in __init__
    self._inferred_dtype = self._validate(data)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/pandas/core/strings/accessor.py", line 235, in _validate
    raise AttributeError("Can only use .str accessor with string values!")
AttributeError: Can only use .str accessor with string values!. Did you mean: 'std'?
exit status 1

[WEIZHI-zheng]

Dear Nagesh,
I have encountered the same issue as you. Might I ask if you have since found a resolution?

[nadluru]

Dear Weizhi,

We later realized it was due to having "EstimatedPhaseEncodingDirection" instead of just "PhaseEncodingDirection" in the JSON files. Hope that is helpful information.

Thank you and kind regards,
Nagesh