Summary of what happened:
Yesterday, I downloaded and used the newly released QSIPrep version 1.0.2. Only the first dataset was processed successfully. Starting from the second dataset, each one failed with the error: “Node synthseg failed to run on host 65d6ab86fcaa.” The same datasets did not have this problem when processed with the previous version of QSIPrep. My system has 40 CPUs and 251.5 GiB of total memory.
Command used (and if a helper script was used, a link to the helper script or the command generated):
docker run --rm -m 50GB\
-v "$INPUT_DIR:/input" \
-v "$WORK_DIR:/work" \
-v "$OUTPUT_DIR:/output" \
pennlinc/qsiprep:1.0.2 \
/input /output participant \
--participant-label KW73020200929 \
--b0-threshold 10 \
--output-resolution 2 \
--hmc-model eddy \
--skip-bids-validation \
--anatomical-template MNI152NLin2009cAsym \
--work-dir /work \
--nprocs 12 \
--omp-nthreads 2
Version:
QSIPrep 1.0.2
Environment (Docker, Singularity / Apptainer, custom installation):
Docker
Data formatted according to a validatable standard? Please provide the output of the validator:
Relevant log outputs (up to 20 lines):
251113-07:37:26,636 nipype.workflow WARNING:
Storing result file without outputs
251113-07:37:26,637 nipype.workflow WARNING:
[Node] Error on "qsiprep_1_0_wf.sub_KW99220190809_wf.anat_preproc_wf.synthseg_wf.synthprep_1_0_wf/sub_KW99220190809_wf/anat_preproc_wf/synthseg_wf/synthseg)
251113-07:37:26,729 nipype.workflow ERROR:
Node synthseg failed to run on host 29d9a3046556.
251113-07:37:26,745 nipype.workflow ERROR:
Saving crash info to /output/sub-KW99220190809/log/20251113-073555_13a6319a-2e58-4b0a-1c/crash-20251113-073726-root-synthseg-c8a2f8c3-df80-4a67-9628-e2c2e0ca168a.txt
Traceback (most recent call last):
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.n run_node
result["result"] = node.run(updatehash=updatehash)
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", n
result = self._run_interface(execute=True)
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", un_interface
return self._run_command(execute)
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", un_command
raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node synthseg
Cmdline:
mri_synthseg --cpu --i /work/qsiprep_1_0_wf/sub_KW99220190809_wf/anat_preproc_wf/dl_prekulled_to_reference/sub-KW99220190809_T1w_lps_trans.nii.gz --threads 1 --post sub-KW99220190809post.nii.gz --qc sub-KW99220190809_T1w_lps_trans_qc.csv --o sub-KW99220190809_T1w_lps_trans_ase
Stdout:
SynthSeg 2.0
using CPU, hiding all CUDA_VISIBLE_DEVICES
using 1 thread
Stderr:
Traceback (most recent call last):
File "/opt/freesurfer/bin/mri_synthseg", line 2581, in <module>
main()
File "/opt/freesurfer/bin/mri_synthseg", line 123, in main
predict(
File "/opt/freesurfer/bin/mri_synthseg", line 195, in predict
labels_segmentation, _ = get_list_labels(label_list=labels_segmentation)
File "/opt/freesurfer/bin/mri_synthseg", line 1446, in get_list_labels
label_list = np.array(reformat_to_list(label_list, load_as_numpy=True, dtype='int')
File "/opt/freesurfer/bin/mri_synthseg", line 1534, in reformat_to_list
if isinstance(var, (int, float, np.int, np.int32, np.int64, np.float, np.float32, n
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/numpy/__init__.py", line 3r__
raise AttributeError(__former_attrs__[attr])
AttributeError: module 'numpy' has no attribute 'int'.
`np.int` was a deprecated alias for the builtin `int`. To avoid this error in existing by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you me.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use,ase note link for additional information.
The aliases was originally deprecated in NumPy 1.20; for more details and guidance see lease note at:
https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations. Did you mean: 'in
Traceback:
Traceback (most recent call last):
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/interfaces/base/cor, in aggregate_outputs
setattr(outputs, key, val)
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/interfaces/base/tray", line 325, in validate
value = super().validate(objekt, name, value, return_pathlike=True)
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/interfaces/base/tray", line 135, in validate
self.error(objekt, name, str(value))
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/traits/base_trait_handler.n error
raise TraitError(
traits.trait_errors.TraitError: The 'out_post' trait of a _SynthSegOutputSpec instance ike object or string representing an existing file, but a value of '/work/qsiprep_1_0_wf/sub_KWanat_preproc_wf/synthseg_wf/synthseg/sub-KW99220190809_T1w_lps_trans_post.nii.gz' <class 'str'>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/interfaces/base/cor, in run
outputs = self.aggregate_outputs(runtime)
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/interfaces/base/cor, in aggregate_outputs
raise FileNotFoundError(msg)
FileNotFoundError: No such file or directory '/work/qsiprep_1_0_wf/sub_KW99220190809_wff/synthseg_wf/synthseg/sub-KW99220190809_T1w_lps_trans_post.nii.gz' for output 'out_post' of a ace