Hi everyone,
I am using qsiprep to preprocess and reconstruct dwi data. pyafq is selected as the reconstruction workflow. It can be preprocessed smoothly, but there is an error in the reconstruction.Is there something that I can do to fix this? Any help would be greatly appreciated.
Many thanks
Command：
qsiprep-docker /home/liziyun/test/Nifti /home/liziyun/test/out1 \
--output_resolution 2 --fs-license-file /home/liziyun/test/license.txt \
--unringing-method mrdegibbs --recon_spec pyafq -w /home/liziyun/test/tt
Version:
0.16.1
log
Node: qsirecon_wf.sub-01_pyAFQ_full.sub_01_ses_001_run_001_space_T1w_desc_preproc_recon_wf.pyAFQ_full.run_afq
Working directory: /scratch/qsirecon_wf/sub-01_pyAFQ_full/sub_01_ses_001_run_001_space_T1w_desc_preproc_recon_wf/pyAFQ_full/run_afq
Node inputs:
bval_file = <undefined>
bvec_file = <undefined>
dwi_file = <undefined>
itk_file = <undefined>
kwargs = {'directions': 'prob', 'max_angle': 30.0, 'sphere': None, 'seed_mask': None, 'seed_threshold': 0, 'n_seeds': 1, 'random_seeds': False, 'rng_seed': None, 'stop_mask': None, 'stop_threshold': 0, 'step_size': 0.5, 'min_length': 10, 'max_length': 1000, 'odf_model': 'CSD', 'tracker': 'local', 'nb_points': False, 'nb_streamlines': False, 'seg_algo': 'AFQ', 'reg_algo': None, 'clip_edges': False, 'parallel_segmentation': {'n_jobs': -1, 'engine': 'joblib', 'backend': 'loky'}, 'progressive': True, 'greater_than': 50, 'rm_small_clusters': 50, 'model_clust_thr': 1.25, 'reduction_thr': 25, 'refine': False, 'pruning_thr': 12, 'b0_threshold': 50, 'prob_threshold': 0, 'roi_dist_tie_break': False, 'dist_to_waypoint': None, 'rng': None, 'return_idx': False, 'presegment_bundle_dict': None, 'presegment_kwargs': {}, 'filter_by_endpoints': True, 'dist_to_atlas': 4, 'save_intermediates': None, 'n_points': 100, 'clean_rounds': 5, 'distance_threshold': 5, 'length_threshold': 4, 'min_sl': 20, 'stat': 'mean', 'min_bval': None, 'max_bval': None, 'filter_b': True, 'robust_tensor_fitting': False, 'csd_response': None, 'csd_sh_order': None, 'csd_lambda_': 1, 'csd_tau': 0.1, 'gtol': 0.01, 'brain_mask_definition': None, 'bundle_info': None, 'reg_template_spec': 'mni_T1', 'mapping_definition': None, 'reg_subject_spec': 'power_map', 'profile_weights': 'gauss', 'scalars': ['dti_fa', 'dti_md'], 'import_tract': None, 'sbv_lims_bundles': [None, None], 'volume_opacity_bundles': 0.3, 'n_points_bundles': 40, 'sbv_lims_indiv': [None, None], 'volume_opacity_indiv': 0.3, 'n_points_indiv': 40, 'viz_backend_spec': 'plotly_no_gif', 'virtual_frame_buffer': False, 'omp_nthreads': 7}
mask_file = <undefined>
tck_file = <undefined>
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 run_afq.
Traceback:
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 398, in run
runtime = self._run_interface(runtime)
File "/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/interfaces/pyafq.py", line 59, in _run_interface
tck_file = fname_presuffix(self.inputs.tck_file,
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/utils/filemanip.py", line 140, in fname_presuffix
pth, fname, ext = split_filename(fname)
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/utils/filemanip.py", line 92, in split_filename
pth = op.dirname(fname)
File "/usr/local/miniconda/lib/python3.8/posixpath.py", line 152, in dirname
p = os.fspath(p)
TypeError: expected str, bytes or os.PathLike object, not _Undefined