sgiavasis
commented
5 years ago Hi @ccraddock,
Thanks for bringing this up- we'll try to reproduce it and get back to you as soon as we can.
Anything specific about the data, or the 64 that crashed, that would be good for us to know?
Best, Steve
Trying to process roughly 120 functional datasets, received similar errors on 64. Looks like to problem is that dimensions of the various arrays in the line:
motionICs = np.squeeze(np.array(np.where((proj > 0) + (csfFract > thr_csf) + (HFC > thr_HFC))))
190322-00:25:10,152 nipype.workflow ERROR: Node aroma_wf.b5 failed to run on host c262-173.hikari.tacc.utexas.edu. 190322-00:25:10,153 nipype.workflow ERROR: Saving crash info to /outputs/crash/crash-20190322-002510-craddock-aroma_wf.b5-c937af2f-faa5-4d67-9471-aeeeb12fe098.pklz Traceback (most recent call last): File "/usr/local/miniconda/lib/python2.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node result['result'] = node.run(updatehash=updatehash) File "/usr/local/miniconda/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 471, in run result = self._run_interface(execute=True) File "/usr/local/miniconda/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 555, in _run_interface return self._run_command(execute) File "/usr/local/miniconda/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_command result = self._interface.run(cwd=outdir) File "/usr/local/miniconda/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 521, in run runtime = self._run_interface(runtime) File "/usr/local/miniconda/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 1033, in _run_interface self.raise_exception(runtime) File "/usr/local/miniconda/lib/python2.7/site-packages/nipype/interfaces/base/core.py", line 970, in raise_exception ).format(**runtime.dictcopy())) RuntimeError: Command: ICA_AROMA.py -den nonaggr -i /scratch/working/resting_preproc_sub-ang1017_ses-1/apply_ants_warp_leaf_node_to_standard_0/_scan_rest_run-01/apply_ants_warp/sub-ang1017_ses-1_task-rest_run-01_bold_calc_tshift_resample_volreg_calc_maths_antswarp.nii.gz -m /scratch/working/resting_preproc_sub-ang1017_ses-1/create_aroma_0/_scan_rest_run-01/bet_aroma/sub-ang1017_ses-1_task-rest_run-01_bold_calc_tshift_resample_volreg_calc_maths_antswarp_brain_mask.nii.gz -mc /scratch/working/resting_preproc_sub-ang1017_ses-1/create_aroma_0/_scan_rest_run-01/par_mcflirt/sub-ang1017_ses-1_task-rest_run-01_bold_calc_tshift_resample_volreg_calc_maths_antswarp_mcf.nii.gz.par -o /scratch/working/resting_preproc_sub-ang1017_ses-1/create_aroma_0 Standard output:
------------------------------- RUNNING ICA-AROMA ------------------------------- --------------- 'ICA-based Automatic Removal Of Motion Artifacts' ---------------
Step 1) MELODIC Step 2) Automatic classification of the components