Open hahaai opened 3 years ago
Here are also a few crash files:
nipypecli crash default_NDARAB348EWR/log/crash-20210211-221048-rbc-build_nuisance_regressors.a1-698aaaa1-38dd-4378-b9c0-fe84a0d36356.pklz
ile: /cbica/projects/RBC/CPACTesting/Pipeline_Timing/Running_problem_testing/AllNew/CPAC_out/default_NDARAB348EWR/log/crash-20210211-221048-rbc-build_nuisance_regressors.a1-698aaaa1-38dd-4378-b9c0-fe84a0d36356.pklz Node: cpacsub-NDARAB348EWR.nuisance_regressors_default_166.build_nuisance_regressors Working directory: /cbica/projects/RBC/CPACTesting/Pipeline_Timing/Running_problem_testing/AllNew/CPAC_out/default_NDARAB348EWR/working/cpacsub-NDARAB348EWR/nuisance_regressors_default_166/_scan_movieTP/build_nuisance_regressors
Node inputs:
acompcor_file_path =
Traceback: Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node result["result"] = node.run(updatehash=updatehash) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run result = self._run_interface(execute=True) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface return self._run_command(execute) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command result = self._interface.run(cwd=outdir) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 419, in run runtime = self._run_interface(runtime) File "/code/CPAC/utils/interfaces/function.py", line 152, in _run_interface out = function_handle(**args) File "/code/CPAC/nuisance/nuisance.py", line 198, in gather_nuisance regressor_length)) ValueError: Number of time points in /cbica/projects/RBC/CPACTesting/Pipeline_Timing/Running_problem_testing/AllNew/CPAC_out/default_NDARAB348EWR/working/cpac__sub-NDARAB348EWR/nuisance_regressors_default_166/_scan_movieTP/CerebrospinalFluid_mean/denoised_func_data_nonaggr_0_trans_tcat_flirt_roistat.1D (0) is inconsistent with length of functional file /cbica/projects/RBC/CPACTesting/Pipeline_Timing/Running_problem_testing/AllNew/CPAC_out/default_NDARAB348EWR/working/cpac__sub-NDARAB348EWR/ICA-AROMA_ANTs_template_to_bold_159/_scan_movieTP/func_concat_ICA-AROMA_ANTs_template_to_bold_159/denoised_func_data_nonaggr_0_trans_tcat.nii.gz (250)I found some crash files in the log folder:
File: /cbica/projects/RBC/CPACTesting/Pipeline_Timing/Running_problem_testing/AllNew/CPAC_out/default_NDARAB348EWR/log/crash-20210211-221048-rbc-build_nuisance_regressors.a1-698aaaa1-38dd-4378-b9c0-fe84a0d36356.pklz Node: cpacsub-NDARAB348EWR.nuisance_regressors_default_166.build_nuisance_regressors Working directory: /cbica/projects/RBC/CPACTesting/Pipeline_Timing/Running_problem_testing/AllNew/CPAC_out/default_NDARAB348EWR/working/cpacsub-NDARAB348EWR/nuisance_regressors_default_166/_scan_movieTP/build_nuisance_regressors
Node inputs:
acompcor_file_path =
Traceback: Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node result["result"] = node.run(updatehash=updatehash) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run result = self._run_interface(execute=True) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface return self._run_command(execute) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command result = self._interface.run(cwd=outdir) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 419, in run runtime = self._run_interface(runtime) File "/code/CPAC/utils/interfaces/function.py", line 152, in _run_interface out = function_handle(**args) File "/code/CPAC/nuisance/nuisance.py", line 198, in gather_nuisance regressor_length)) ValueError: Number of time points in /cbica/projects/RBC/CPACTesting/Pipeline_Timing/Running_problem_testing/AllNew/CPAC_out/default_NDARAB348EWR/working/cpac__sub-NDARAB348EWR/nuisance_regressors_default_166/_scan_movieTP/CerebrospinalFluid_mean/denoised_func_data_nonaggr_0_trans_tcat_flirt_roistat.1D (0) is inconsistent with length of functional file /cbica/projects/RBC/CPACTesting/Pipeline_Timing/Running_problem_testing/AllNew/CPAC_out/default_NDARAB348EWR/working/cpac__sub-NDARAB348EWR/ICA-AROMA_ANTs_template_to_bold_159/_scan_movieTP/func_concat_ICA-AROMA_ANTs_template_to_bold_159/denoised_func_data_nonaggr_0_trans_tcat.nii.gz (250)I found some crash files in the log folder:
File: /cbica/projects/RBC/CPACTesting/Pipeline_Timing/Running_problem_testing/AllNew/CPAC_out/default_NDARAB348EWR/log/crash-20210211-221048-rbc-build_nuisance_regressors.a1-698aaaa1-38dd-4378-b9c0-fe84a0d36356.pklz Node: cpacsub-NDARAB348EWR.nuisance_regressors_default_166.build_nuisance_regressors Working directory: /cbica/projects/RBC/CPACTesting/Pipeline_Timing/Running_problem_testing/AllNew/CPAC_out/default_NDARAB348EWR/working/cpacsub-NDARAB348EWR/nuisance_regressors_default_166/_scan_movieTP/build_nuisance_regressors
Node inputs:
acompcor_file_path =
Traceback: Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node result["result"] = node.run(updatehash=updatehash) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run result = self._run_interface(execute=True) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface return self._run_command(execute) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command result = self._interface.run(cwd=outdir) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 419, in run runtime = self._run_interface(runtime) File "/code/CPAC/utils/interfaces/function.py", line 152, in _run_interface out = function_handle(**args) File "/code/CPAC/nuisance/nuisance.py", line 198, in gather_nuisance regressor_length)) ValueError: Number of time points in /cbica/projects/RBC/CPACTesting/Pipeline_Timing/Running_problem_testing/AllNew/CPAC_out/default_NDARAB348EWR/working/cpac__sub-NDARAB348EWR/nuisance_regressors_default_166/_scan_movieTP/CerebrospinalFluid_mean/denoised_func_data_nonaggr_0_trans_tcat_flirt_roistat.1D (0) is inconsistent with length of functional file /cbica/projects/RBC/CPACTesting/Pipeline_Timing/Running_problem_testing/AllNew/CPAC_out/default_NDARAB348EWR/working/cpac__sub-NDARAB348EWR/ICA-AROMA_ANTs_template_to_bold_159/_scan_movieTP/func_concat_ICA-AROMA_ANTs_template_to_bold_159/denoised_func_data_nonaggr_0_trans_tcat.nii.gz (250)I found some crash files in the log folder:
File: /cbica/projects/RBC/CPACTesting/Pipeline_Timing/Running_problem_testing/AllNew/CPAC_out/default_NDARAB348EWR/log/crash-20210211-221048-rbc-build_nuisance_regressors.a1-698aaaa1-38dd-4378-b9c0-fe84a0d36356.pklz Node: cpacsub-NDARAB348EWR.nuisance_regressors_default_166.build_nuisance_regressors Working directory: /cbica/projects/RBC/CPACTesting/Pipeline_Timing/Running_problem_testing/AllNew/CPAC_out/default_NDARAB348EWR/working/cpacsub-NDARAB348EWR/nuisance_regressors_default_166/_scan_movieTP/build_nuisance_regressors
Node inputs:
acompcor_file_path =
Traceback: Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node result["result"] = node.run(updatehash=updatehash) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run result = self._run_interface(execute=True) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface return self._run_command(execute) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command result = self._interface.run(cwd=outdir) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 419, in run runtime = self._run_interface(runtime) File "/code/CPAC/utils/interfaces/function.py", line 152, in _run_interface out = function_handle(**args) File "/code/CPAC/nuisance/nuisance.py", line 198, in gather_nuisance regressor_length)) ValueError: Number of time points in /cbica/projects/RBC/CPACTesting/Pipeline_Timing/Running_problem_testing/AllNew/CPAC_out/default_NDARAB348EWR/working/cpac__sub-NDARAB348EWR/nuisance_regressors_default_166/_scan_movieTP/CerebrospinalFluid_mean/denoised_func_data_nonaggr_0_trans_tcat_flirt_roistat.1D (0) is inconsistent with length of functional file /cbica/projects/RBC/CPACTesting/Pipeline_Timing/Running_problem_testing/AllNew/CPAC_out/default_NDARAB348EWR/working/cpac__sub-NDARAB348EWR/ICA-AROMA_ANTs_template_to_bold_159/_scan_movieTP/func_concat_ICA-AROMA_ANTs_template_to_bold_159/denoised_func_data_nonaggr_0_trans_tcat.nii.gz (250)
Another crash file type:
nipypecli crash default_NDARAB348EWR/log/crash-20210211-215342-rbc-chunk_warp_ts_to_T1template_205.a0-8e108e9c-661b-4735-b9f0-7e975af67f2c.pklz
File: /cbica/projects/RBC/CPACTesting/Pipeline_Timing/Running_problem_testing/AllNew/CPAC_out/default_NDARAB348EWR/log/crash-20210211-215342-rbc-chunk_warp_ts_to_T1template_205.a0-8e108e9c-661b-4735-b9f0-7e975af67f2c.pklz Node: cpacsub-NDARAB348EWR.warp_ts_to_T1template_205.chunk_warp_ts_to_T1template_205 Working directory: /cbica/projects/RBC/CPACTesting/Pipeline_Timing/Running_problem_testing/AllNew/CPAC_out/default_NDARAB348EWR/working/cpacsub-NDARAB348EWR/warp_ts_to_T1template_205/_scan_movieDM/chunk_warp_ts_to_T1template_205
Node inputs:
func_file =
for chunk_idx in range(0, n_cpus):
if chunk_idx == n_cpus - 1:
TR_ranges.append((int(chunk_idx*chunk), int(trs - 1)))
else:
TR_ranges.append((int(chunk_idx*chunk), int((chunk_idx+1)*chunk -1)))
return TR_ranges
n_cpus = 8
Traceback:
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
return self._run_command(execute)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
result = self._interface.run(cwd=outdir)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 419, in run
runtime = self._run_interface(runtime)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/utility/wrappers.py", line 142, in _run_interface
out = function_handle(**args)
File "
pipelines used mcflirt
(fmriprep and XCP) also has the following crash file:
nipypecli crash fmriprep_NDARAB348EWR/log/crash-20210211-213148-rbc-get_mcflirt_rms_abs_90-c1eee511-cff5-4fc7-b2bc-204c595b2a3f.pklz
File: /cbica/projects/RBC/CPACTesting/Pipeline_Timing/Running_problem_testing/AllNew/CPAC_out/fmriprep_NDARAB348EWR/log/crash-20210211-213148-rbc-get_mcflirt_rms_abs_90-c1eee511-cff5-4fc7-b2bc-204c595b2a3f.pklz Node: cpac__sub-NDARAB348EWR.get_mcflirt_rms_abs_90 Working directory: /cbica/projects/RBC/CPACTesting/Pipeline_Timing/Running_problem_testing/AllNew/CPAC_out/fmriprep_NDARAB348EWR/working/cpac__sub-NDARAB348EWR/get_mcflirt_rms_abs_90
Node inputs:
function_str = def get_mcflirt_rms_abs(rms_files): for path in rms_files: if 'abs.rms' in path: return path
rms_files =
Traceback: Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node result["result"] = node.run(updatehash=updatehash) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run result = self._run_interface(execute=True) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface return self._run_command(execute) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command result = self._interface.run(cwd=outdir) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 419, in run runtime = self._run_interface(runtime) File "/code/CPAC/utils/interfaces/function.py", line 152, in _run_interface out = function_handle(**args) TypeError: get_mcflirt_rms_abs() missing 1 required positional argument: 'rms_files'
ValueError: Number of time points in /cbica/projects/RBC/CPACTesting/Pipeline_Timing/Running_problem_testing/AllNew/CPAC_out/default_NDARAB348EWR/working/cpac__sub-NDARAB348EWR/nuisance_regressors_default_166/_scan_movieTP/CerebrospinalFluid_mean/denoised_func_data_nonaggr_0_trans_tcat_flirt_roistat.1D (0) is inconsistent with length of functional file
I wonder if this is a data quality issue or if something isn't mapping correctly. It looks like it's creating 0-length ROI files.
ValueError: Number of time points in /cbica/projects/RBC/CPACTesting/Pipeline_Timing/Running_problem_testing/AllNew/CPAC_out/default_NDARAB348EWR/working/cpac__sub-NDARAB348EWR/nuisance_regressors_default_166/_scan_movieTP/CerebrospinalFluid_mean/denoised_func_data_nonaggr_0_trans_tcat_flirt_roistat.1D (0) is inconsistent with length of functional file
I wonder if this is a data quality issue or if something isn't mapping correctly. It looks like it's creating 0-length ROI files.
Actually this the lateral ventrical problem where the reference has 3 volume in it rather than 1. This has beee fixed.
C-PAC Run Info
Include:
pipeline_configs.zip
Developers only:
ster/corr_two_1D.py) but heatmaps or other visualizations are good too):