Qsiprep dwibiascorrect error

halil_aziz_velioglu · April 6, 2023, 4:14pm

Summary of what happened:

Hello,
I am running qsiprep via docker but getting dwibiascorrect error. In my BIDS dataset dwi folder there are dwi.nii.gz, dwi.bval, dwi.bvec. dwi.sjon, sbref.json and sbref.nii.gz.

Command used (and if a helper script was used, a link to the helper script or the command generated):

docker run --rm -v /analysis/halilaziz/bids_raw:/data -v /analysis/halilaziz/processout:/output -v /usr/local/local/opt/freesurfer6/license.txt:/usr/local/local/opt/freesurfer6/license.txt pennbbl/qsiprep:latest /data /output participant --participant-label 12121 --nthreads 8 --omp-nthreads 8 --mem-mb 16000 --skip_bids_validation --fs-license-file /usr/local/local/opt/freesurfer6/license.txt --output-resolution 1.2

Version:

I am using qsiprep v0.17.0

Environment (Docker, Singularity, custom installation):

Docker

Data formatted according to a validatable standard? Please provide the output of the validator:

Relevant log outputs (up to 20 lines):

Screenshots / relevant information:

Steven · April 6, 2023, 5:22pm

Hi @halil_aziz_velioglu, and welcome to neurostars!

Please provide the log output that describes the error, and whether your data pass BIDS validation.

Best,
Steven

halil_aziz_velioglu · April 6, 2023, 6:36pm

Hello Steven
Thank you your message.
Here is

QSIPrep failed: Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py                               ", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", li                               ne 527, in run
    result = self._run_interface(execute=True)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", li                               ne 645, in _run_interface
    return self._run_command(execute)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", li                               ne 771, in _run_command
    raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node biasco                               rr.

Cmdline:
        dwibiascorrect ants -ants.b [150,3] -ants.c [200x200,1e-6] -bias sub-12193_dwi_denois                               ed_bias.nii.gz -fslgrad /data/sub-12193/dwi/sub-12193_dwi.bvec /data/sub-12193/dwi/sub-12193_                               dwi.bval -mask /tmp/work/qsiprep_wf/single_subject_12193_wf/dwi_preproc_wf/pre_hmc_wf/merge_a                               nd_denoise_wf/dwi_denoise_dwi_wf/quick_mask/sub-12193_dwi_denoised_b0_series_mask.nii.gz /tmp                               /work/qsiprep_wf/single_subject_12193_wf/dwi_preproc_wf/pre_hmc_wf/merge_and_denoise_wf/dwi_d                               enoise_dwi_wf/denoiser/sub-12193_dwi_denoised.nii.gz sub-12193_dwi_denoised_N4.nii.gz
Stdout:

Stderr:
        dwibiascorrect:
        dwibiascorrect: Note that this script makes use of commands / algorithms that have re                               levant articles for citation; INCLUDING FROM EXTERNAL SOFTWARE PACKAGES. Please consult the h                               elp page (-help option) for more information.
        dwibiascorrect:
        dwibiascorrect: Generated scratch directory: /tmp/work/qsiprep_wf/single_subject_1219                               3_wf/dwi_preproc_wf/pre_hmc_wf/merge_and_denoise_wf/dwi_denoise_dwi_wf/biascorr/dwibiascorrec                               t-tmp-PAGK26/
        Command:  mrconvert /tmp/work/qsiprep_wf/single_subject_12193_wf/dwi_preproc_wf/pre_h                               mc_wf/merge_and_denoise_wf/dwi_denoise_dwi_wf/denoiser/sub-12193_dwi_denoised.nii.gz /tmp/wor                               k/qsiprep_wf/single_subject_12193_wf/dwi_preproc_wf/pre_hmc_wf/merge_and_denoise_wf/dwi_denoi                               se_dwi_wf/biascorr/dwibiascorrect-tmp-PAGK26/in.mif -fslgrad /data/sub-12193/dwi/sub-12193_dw                               i.bvec /data/sub-12193/dwi/sub-12193_dwi.bval
        Command:  mrconvert /tmp/work/qsiprep_wf/single_subject_12193_wf/dwi_preproc_wf/pre_h                               mc_wf/merge_and_denoise_wf/dwi_denoise_dwi_wf/quick_mask/sub-12193_dwi_denoised_b0_series_mas                               k.nii.gz /tmp/work/qsiprep_wf/single_subject_12193_wf/dwi_preproc_wf/pre_hmc_wf/merge_and_den                               oise_wf/dwi_denoise_dwi_wf/biascorr/dwibiascorrect-tmp-PAGK26/mask.mif -datatype bit
        dwibiascorrect: Changing to scratch directory (/tmp/work/qsiprep_wf/single_subject_12                               193_wf/dwi_preproc_wf/pre_hmc_wf/merge_and_denoise_wf/dwi_denoise_dwi_wf/biascorr/dwibiascorr                               ect-tmp-PAGK26/)
        Command:  dwiextract in.mif - -bzero | mrmath - mean mean_bzero.mif -axis 3

        dwibiascorrect: [ERROR] dwiextract in.mif - -bzero | mrmath - mean mean_bzero.mif -ax                               is 3 (ants.py:64)
        dwibiascorrect: [ERROR] Information from failed command:
        dwibiascorrect:
                        dwiextract: [ERROR] No b=0 volumes present
                        mrmath: [ERROR] no filename supplied to standard input (broken pipe?)
                        mrmath: [ERROR] error opening image "-"
        dwibiascorrect:
        dwibiascorrect: [ERROR] For debugging, inspect contents of scratch directory: /tmp/wo                               rk/qsiprep_wf/single_subject_12193_wf/dwi_preproc_wf/pre_hmc_wf/merge_and_denoise_wf/dwi_deno                               ise_dwi_wf/biascorr/dwibiascorrect-tmp-PAGK26/
        dwibiascorrect: Scratch directory retained; location: /tmp/work/qsiprep_wf/single_sub                               ject_12193_wf/dwi_preproc_wf/pre_hmc_wf/merge_and_denoise_wf/dwi_denoise_dwi_wf/biascorr/dwib                               iascorrect-tmp-PAGK26/

Steven · April 6, 2023, 6:39pm

Seems like your DWI image has no b0 images. Is this true, looking at your bval file? Also, what about BIDS validaition?

halil_aziz_velioglu · April 6, 2023, 6:51pm

Actually I looked at the bval file there is no b0. However, I think qsiprep should have used sbref.nii.gz image as b0 right?
I think I need to install npm install -g npm@9.6.4 for the BIDS validation

Steven · April 6, 2023, 6:59pm

No, QSIPrep does not substitute the sbref for b0. The b0 is expected to be part of your DWI image. QSIPrep ignores DWI sbrefs entirely. I do not know a priori if your sbref would function well as a b0.

You can remove --skip-bids-validation in your QSIPrep command, or try one of the methods below:

Best,
Steven

halil_aziz_velioglu · April 6, 2023, 7:01pm

Ok Thank you for your help
I will try it