yarikoptic
commented
1 month ago I wish I pasted a full output because I think I ran into this again
(dev3) yoh@typhon:/data/yoh/1076_spacetop$ docker run -it --entrypoint bash --user $(id -u):$(id -g) -v $PWD:$PWD -w $PWD --entrypoint bash bidsonym:local bash-5.2$ pwd
/data/yoh/1076_spacetop
bash-5.2$ bidsonym . participant --brainextraction bet --bet_frac 0.5 --skip_bids_validation --participant_label 0001 0002
Input data will not be checked for BIDS compliance.
Found the following session(s) for participant 0001:
['01', '02', '03', '04']
...
240612-17:26:41,457 nipype.workflow ERROR:
Saving crash info to /data/yoh/1076_spacetop/crash-20240612-172641-UID47521-bet-a3e9c725-39ac-4eff-a063-9df349e73348.pklz
Traceback (most recent call last):
File "/opt/miniconda-latest/lib/python3.11/site-packages/nipype/pipeline/plugins/linear.py", line 47, in run
node.run(updatehash=updatehash)
File "/opt/miniconda-latest/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
result = self._run_interface(execute=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/miniconda-latest/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
return self._run_command(execute)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/miniconda-latest/lib/python3.11/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 bet.
Cmdline:
bet sub-0001_ses-01_acq-MPRAGEXp3X08mm_T1w.nii.gz sourcedata/bidsonym/sub-0001/sub-0001_ses-01_acq-MPRAGEXp3X08mm_T1w_brainmask_desc-nondeid.nii.gz -f 0.50
Stdout:
/opt/fsl-6.0.7.4/bin/bet failed during command:sub-0001_ses-01_acq-MPRAGEXp3X08mm_T1w.nii.gz sourcedata/bidsonym/sub-0001/sub-0001_ses-01_acq-MPRAGEXp3X08mm_T1w_brainmask_desc-nondeid.nii.gz -f 0.50
bash-5.2$ nipypecli crash crash-20240612-172641-UID47521-bet-a3e9c725-39ac-4eff-a063-9df349e73348.pklz
File: /data/yoh/1076_spacetop/crash-20240612-172641-UID47521-bet-a3e9c725-39ac-4eff-a063-9df349e73348.pklz
Node: brainextraction_wf.bet
Working directory: /tmp/tmpzwjsmxnu/brainextraction_wf/bet
Node inputs:
args = <undefined>
center = <undefined>
environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
frac = 0.5
functional = <undefined>
in_file = /tmp/tmpzwjsmxnu/brainextraction_wf/bet/sub-0001_ses-01_acq-MPRAGEXp3X08mm_T1w.nii.gz
mask = False
mesh = <undefined>
no_output = <undefined>
out_file = sourcedata/bidsonym/sub-0001/sub-0001_ses-01_acq-MPRAGEXp3X08mm_T1w_brainmask_desc-nondeid.nii.gz
...so while in a temp folder for the node it was trying to write into "relative" to the top of the dataset path (although it is also odd that it takes it as output for bet but it is under sourcedata/ so there might be more to the bug...). I will now redo with full path
Running
lead to the crash (sorry -- not cut pasting - needs sensoring of paths) unable to find the file with relative path under
sourcedata/. Providing full path resolved it.