Trying to run MRIQC (v0.15.1) on what seems a valid BIDS directory that contains both anat and func. The outputs for the _bold files are produced. However, it fails for the anat for all subjects. Crash log is below.
[AP2-TAU] (env) winkleram@cn1499:~/Projects/AP2-TAU/temp/mriqc/AP2/s1620.out/logs $ cat crash-20200108-180040-winkleram-ComputeQI2.a0-542d78bd-8e68-49e5-9a83-fa737bf9cc1e.txt
Node: workflow_enumerator.anatMRIQCT1w.ComputeIQMs.ComputeQI2
Working directory: /lscratch/45856461/s1620.wrk/workflow_enumerator/anatMRIQCT1w/ComputeIQMs/_in_file_..gpfs..gsfs4..users..kircanskik..AP2-TAU..BIDS..AP2..sub-s1620..anat..sub-s1620_T1w.nii.gz/ComputeQI2
Node inputs:
air_msk = /lscratch/45856461/s1620.wrk/workflow_enumerator/anatMRIQCT1w/AirMaskWorkflow/_in_file_..gpfs..gsfs4..users..kircanskik..AP2-TAU..BIDS..AP2..sub-s1620..anat..sub-s1620_T1w.nii.gz/ArtifactMask/sub-s1620_T1w_conformed_hat.nii.gz
in_file = /lscratch/45856461/s1620.wrk/workflow_enumerator/anatMRIQCT1w/_in_file_..gpfs..gsfs4..users..kircanskik..AP2-TAU..BIDS..AP2..sub-s1620..anat..sub-s1620_T1w.nii.gz/conform/sub-s1620_T1w_conformed.nii.gz
Traceback (most recent call last):
File "/gpfs/gsfs4/users/kircanskik/AP2-TAU/code/env/lib/python3.7/site-packages/nipype/pipeline/plugins/linear.py", line 46, in run
node.run(updatehash=updatehash)
File "/gpfs/gsfs4/users/kircanskik/AP2-TAU/code/env/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
result = self._run_interface(execute=True)
File "/gpfs/gsfs4/users/kircanskik/AP2-TAU/code/env/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
return self._run_command(execute)
File "/gpfs/gsfs4/users/kircanskik/AP2-TAU/code/env/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
result = self._interface.run(cwd=outdir)
File "/gpfs/gsfs4/users/kircanskik/AP2-TAU/code/env/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 395, in run
runtime = self._run_interface(runtime)
File "/gpfs/gsfs4/users/kircanskik/AP2-TAU/code/env/lib/python3.7/site-packages/mriqc/interfaces/anatomical.py", line 292, in _run_interface
qi2, out_file = art_qi2(imdata, airdata)
File "/gpfs/gsfs4/users/kircanskik/AP2-TAU/code/env/lib/python3.7/site-packages/mriqc/qc/anatomical.py", line 437, in art_qi2
from mriqc.viz.misc import plot_qi2
File "/gpfs/gsfs4/users/kircanskik/AP2-TAU/code/env/lib/python3.7/site-packages/mriqc/viz/misc.py", line 18, in <module>
from ..classifier.sklearn.preprocessing import BatchRobustScaler
File "/gpfs/gsfs4/users/kircanskik/AP2-TAU/code/env/lib/python3.7/site-packages/mriqc/classifier/sklearn/__init__.py", line 5, in <module>
from .cv_nested import ModelAndGridSearchCV
File "/gpfs/gsfs4/users/kircanskik/AP2-TAU/code/env/lib/python3.7/site-packages/mriqc/classifier/sklearn/cv_nested.py", line 29, in <module>
from sklearn.model_selection._validation import (
ImportError: cannot import name '_index_param_value' from 'sklearn.model_selection._validation' (/gpfs/gsfs4/users/kircanskik/AP2-TAU/code/env/lib/python3.7/site-packages/sklearn/model_selection/_validation.py)
Btw, scikit-learn is installed:
pip install sklearn
Requirement already satisfied: sklearn in /gpfs/gsfs4/users/kircanskik/AP2-TAU/code/env/lib/python3.7/site-packages (0.0)
Requirement already satisfied: scikit-learn in /gpfs/gsfs4/users/kircanskik/AP2-TAU/code/env/lib/python3.7/site-packages (from sklearn) (0.22.1)
Requirement already satisfied: scipy>=0.17.0 in /gpfs/gsfs4/users/kircanskik/AP2-TAU/code/env/lib/python3.7/site-packages (from scikit-learn->sklearn) (1.4.1)
Requirement already satisfied: numpy>=1.11.0 in /gpfs/gsfs4/users/kircanskik/AP2-TAU/code/env/lib/python3.7/site-packages (from scikit-learn->sklearn) (1.18.0)
Requirement already satisfied: joblib>=0.11 in /gpfs/gsfs4/users/kircanskik/AP2-TAU/code/env/lib/python3.7/site-packages (from scikit-learn->sklearn) (0.14.1)