Hello there,
I have a similar problem than Renaud with 14/69 raw_gqi crashes :
- no html report
- QC files missing (
.jsonand.csv)
and the following output files for these subjects :
├── anat
│ ├── sub-VS006_desc-brain_mask.nii.gz
│ ├── sub-VS006_desc-preproc_T1w.nii.gz
│ ├── sub-VS006_dseg.nii.gz
│ ├── sub-VS006_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5
│ ├── sub-VS006_from-orig_to-T1w_mode-image_xfm.txt
│ ├── sub-VS006_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5
│ ├── sub-VS006_label-CSF_probseg.nii.gz
│ ├── sub-VS006_label-GM_probseg.nii.gz
│ ├── sub-VS006_label-WM_probseg.nii.gz
│ ├── sub-VS006_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
│ ├── sub-VS006_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz
│ ├── sub-VS006_space-MNI152NLin2009cAsym_dseg.nii.gz
│ ├── sub-VS006_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz
│ ├── sub-VS006_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz
│ └── sub-VS006_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz
├── dwi
│ ├── sub-VS006_acq-cusp66b3000_dir-ap_confounds.tsv
│ ├── sub-VS006_acq-cusp66b3000_dir-ap_desc-SliceQC_dwi.json
│ ├── sub-VS006_acq-cusp66b3000_dir-ap_space-T1w_desc-brain_mask.nii.gz
│ ├── sub-VS006_acq-cusp66b3000_dir-ap_space-T1w_desc-eddy_cnr.nii.gz
│ ├── sub-VS006_acq-cusp66b3000_dir-ap_space-T1w_desc-preproc_dwi.b
│ ├── sub-VS006_acq-cusp66b3000_dir-ap_space-T1w_desc-preproc_dwi.bval
│ ├── sub-VS006_acq-cusp66b3000_dir-ap_space-T1w_desc-preproc_dwi.bvec
│ ├── sub-VS006_acq-cusp66b3000_dir-ap_space-T1w_desc-preproc_dwi.nii.gz
│ └── sub-VS006_acq-cusp66b3000_dir-ap_space-T1w_dwiref.nii.gz
└── log
└── 20221105-152554_af0435b2-876a-4aac-a075-3d36cd797b3c
└── crash-20221105-181856-qduche-raw_gqi-0bd9638d-0e58-4dcd-9b46-5bf380c60732.txt
Example of a crash txt file
Node: qsiprep_wf.single_subject_VS025_wf.dwi_finalize_acq_cusp66b3000_dir_ap_wf.transform_dwis_t1.calculate_qc.raw_gqi
Working directory: /work/qsiprep_wf/single_subject_VS025_wf/dwi_finalize_acq_cusp66b3000_dir_ap_wf/transform_dwis_t1/calculate_qc/raw_gqi
Node inputs:
args = <undefined>
check_btable = 0
decomp_fraction = <undefined>
decomp_m_value = <undefined>
decomposition = <undefined>
deconv_regularization = <undefined>
deconvolution = <undefined>
environ = {}
grad_dev = <undefined>
input_src_file = /work/qsiprep_wf/single_subject_VS025_wf/dwi_finalize_acq_cusp66b3000_dir_ap_wf/transform_dwis_t1/calculate_qc/raw_src/vol0000_trans_merged.src.gz
mask = <undefined>
num_fibers = 3
num_threads = 1
odf_order = 8
output_odf = True
ratio_of_mean_diffusion_distance = 1.25
thread_count = 1
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", line 527, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
return self._run_command(execute)
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command
raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node raw_gqi.
Cmdline:
dsi_studio --action=rec --method=4 --check_btable=0 --source=/work/qsiprep_wf/single_subject_VS025_wf/dwi_finalize_acq_cusp66b3000_dir_ap_wf/transform_dwis_t1/calculate_qc/raw_gqi/vol0000_trans_merged.src.gz --num_fiber=3 --thread_count=1 --record_odf=1 --param0=1.2500 --thread_count=1
Stdout:
DSI Studio Feb 22 2022, Fang-Cheng Yeh
source=/work/qsiprep_wf/single_subject_VS025_wf/dwi_finalize_acq_cusp66b3000_dir_ap_wf/transform_dwis_t1/calculate_qc/raw_gqi/vol0000_trans_merged.src.gz
action=rec
loading source...
src loaded
method=4
method=4
param0=1.2500
param0=1.25
odf_order=8
odf_resolving=0
record_odf=1
check_btable=0
output_tensor=0
output_rdi=1
num_fiber=3
r2_weighted=0
csf_calibration=0
thread_count=1
half_sphere=0
scheme_balance=1
record ODF in the fib file
motion_correction=0
start reconstruction...
GQI reconstruction
ERROR:unknown exception
Warning: --thread_count is not used. Please check command line syntax.
Stderr:
Traceback:
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 401, in run
outputs = self.aggregate_outputs(runtime)
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 430, in aggregate_outputs
predicted_outputs = self._list_outputs() # Predictions from _list_outputs
File "/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/interfaces/dsi_studio.py", line 252, in _list_outputs
assert len(results) == 1
AssertionError
My dataset is more detailed here.
Do you have any idea where this can come from ?
Thank you for your help
Quentin