Closed araikes closed 1 week ago
Testing #151. Ran into the following
Node: qsirecon_0_0_wf.sub-011_mrtrix_multishell_msmt_hsvs.recon_anatomical_wf_0.ds_fs_5tt_hsvs Working directory: /xdisk/adamraikes/PD_allo/derivatives/qsirecon_unstable/sessionwise/reports_session/scratch/qsirecon_0_0_wf/sub-011_mrtrix_multishell_msmt_hsvs/recon_anatomical_wf_0/ds_fs_5tt_hsvs Node inputs: acquisition = <undefined> atlas = <undefined> base_directory = /xdisk/adamraikes/PD_allo/derivatives/qsirecon_unstable/sessionwise/reports_session bundle = <undefined> bundles = <undefined> ceagent = <undefined> check_hdr = True chunk = <undefined> cohort = <undefined> compress = [True] data_dtype = <undefined> datatype = <undefined> den = <undefined> desc = <undefined> direction = <undefined> dismiss_entities = ['desc'] echo = <undefined> extension = <undefined> flip = <undefined> fmap = <undefined> from = <undefined> hemi = <undefined> in_file = ['/xdisk/adamraikes/PD_allo/derivatives/qsirecon_unstable/sessionwise/reports_session/scratch/qsirecon_0_0_wf/sub-011_mrtrix_multishell_msmt_hsvs/recon_anatomical_wf_0/create_5tt_hsvs/sub-011_ses-01.long_5tt.mif'] inv = <undefined> label = <undefined> meta_dict = <undefined> modality = <undefined> mode = <undefined> model = <undefined> mt = <undefined> nucleus = <undefined> param = <undefined> part = <undefined> proc = <undefined> reconstruction = <undefined> recording = <undefined> res = <undefined> roi = <undefined> run = <undefined> sample = <undefined> scans = <undefined> seg = hsvs session = <undefined> source_file = ['/xdisk/adamraikes/PD_allo/derivatives/qsiprep_unstable/sessionwise/sub-011/ses-01/anat/sub-011_ses-01_space-ACPC_desc-preproc_T1w.nii.gz'] space = fsnative staining = <undefined> subject = <undefined> subset = <undefined> suffix = probseg task = <undefined> to = <undefined> tracer = <undefined> tracksys = <undefined> volume = <undefined> Traceback (most recent call last): File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 344, in _send_procs_to_workers self.procs[jobid].run(updatehash=updatehash) File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run result = self._run_interface(execute=True) File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface return self._run_command(execute) File "/opt/conda/envs/qsiprep/lib/python3.10/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 ds_fs_5tt_hsvs. Traceback: Traceback (most recent call last): File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 397, in run runtime = self._run_interface(runtime) File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/niworkflows/interfaces/bids.py", line 632, in _run_interface raise ValueError(f"Could not build path with entities {out_entities}.") ValueError: Could not build path with entities {'subject': '011', 'session': '01', 'space': 'fsnative', 'suffix': 'probseg', 'datatype': 'anat', 'extension': 'long_5tt.mif.gz', 'seg': 'hsvs'}.
I think the extension should just be .mif.gz, not long_5tt.mif.gz. We can probably fix this by hardcoding the extension in the DerivativesDataSink.
.mif.gz
long_5tt.mif.gz
Testing #151. Ran into the following