[BUG] select_gradients node breaks custom ss3t yaml pipeline.

[chiuhoward]

Summary

When I used the new yaml files that include this chunk, I get an error

-   action: select_gradients
    input: qsirecon
    name: select_single_shell
    parameters:
        requested_shells:
            - 0
            - highest
        bval_distance_cutoff: 100

I reran my exact same shell script with the old yaml file without this chunk and it executes.

Additional details

• QSIRecon version: 1.0.0rc3.dev0+g619341b.d20241121
• Docker version: NA
• Singularity version: 1.3.2-1.el7 (Apptainer)

What were you trying to do?

I was trying to run a custom ss3t_noACT pipeline by customizing my yaml file. I downloaded the latest yaml file from the qsirecon repo but did not notice that there was an additional node included and my code crashed.

What did you expect to happen?

I expected my code to run as per usual.

What actually happened?

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/qsirecon/cli/workflow.py", line 133, in build_workflow
    retval["workflow"] = init_qsirecon_wf()
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsirecon/workflows/base.py", line 44, in init_qsirecon_wf
    single_subject_wf = init_single_subject_recon_wf(subject_id=subject_id)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsirecon/workflows/base.py", line 268, in init_single_subject_recon_wf
    dwi_recon_wfs[dwi_file] = init_dwi_recon_workflow(
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsirecon/workflows/recon/build_workflow.py", line 70, in init_dwi_recon_workflow
    new_node = workflow_from_spec(
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsirecon/workflows/recon/build_workflow.py", line 290, in workflow_from_spec
    raise Exception("Unknown node %s" % node_spec)
Exception: Unknown node {'action': 'select_gradients', 'input': 'qsirecon', 'name': 'select_single_shell', 'parameters': {'requested_shells': [0, 'highest'], 'bval_distance_cutoff': 100}}

Reproducing the bug

This shell script ran with the first yaml file but not the second (I modified the absolute yaml path in the shell script to point to either):

export APPTAINERENV_FS_LICENSE=$GROUP_HOME/freesurferlicense.txt

singularity run --writable-tmpfs --cleanenv \
/home/groups/jyeatman/software/singularity_images/qsirecon-1.0.0rc2.sif \
/scratch/groups/jyeatman/howard/DBPFullwT1derivNov24-mrdegibbs-ignorefmap \
/scratch/groups/jyeatman/howard/DBPFullwT1derivNov24-mrdegibbs-ignorefmap-recon-sl/ participant --participant-label sub-$SLURM_ARRAY_TASK_ID \
-w /scratch/groups/jyeatman/howard/DBPFullwT1derivNov24-mrdegibbs-ignorefmap-recon-sl-work \
--infant \
--recon-spec /home/groups/jyeatman/software/howard/mrtrix_singleshell_ss3t_noACT_noselectgrad.yaml \
--fs-license-file $GROUP_HOME/freesurferlicense.txt \
--output-resolution 2 \
-v -v

This works:

anatomical: []
name: mrtrix_singleshell_ss3t_noACT
nodes:
-   action: csd
    input: qsirecon
    name: ss3t_csd
    parameters:
        fod:
            algorithm: ss3t
        mtnormalize: true
        response:
            algorithm: dhollander
    qsirecon_suffix: MRtrix3_fork-SS3T_act-None
    software: MRTrix3
-   action: tractography
    input: ss3t_csd
    name: track_ifod2
    parameters:
        sift2: {}
        tckgen:
            algorithm: iFOD2
            quiet: true
            select: 20000000.0
        use_5tt: false
        use_sift2: true
    qsirecon_suffix: MRtrix3_fork-SS3T_act-None
    software: MRTrix3
space: T1w

This didn't:

anatomical: []
name: mrtrix_singleshell_ss3t_noACT
nodes:

-   action: select_gradients
    input: qsirecon
    name: select_single_shell
    parameters:
        requested_shells:
            - 0
            - highest
        bval_distance_cutoff: 100

-   action: csd
    input: select_single_shell
    name: ss3t_csd
    parameters:
        fod:
            algorithm: ss3t
        mtnormalize: true
        response:
            algorithm: dhollander
    qsirecon_suffix: MRtrix3_fork-SS3T_act-None
    software: MRTrix3
-   action: tractography
    input: ss3t_csd
    name: track_ifod2
    parameters:
        sift2: {}
        tckgen:
            algorithm: iFOD2
            max_length: 250
            min_length: 30
            quiet: true
            select: 20000000.0
        use_5tt: false
        use_sift2: true
    qsirecon_suffix: MRtrix3_fork-SS3T_act-None
    software: MRTrix3
space: T1w

[chiuhoward]

Sorry I think #194 will fix this, I'll try again by pulling the latest container and update.

[chiuhoward]

Error goes away in 1.0.0rc3.dev2+gf95211a.d20241206!