C-PAC v1.8.0.dev - fmriprep-options preconfig

[shnizzedy]

C-PAC Run Info

Description	fmriprep-options preconfig
Version	v1.8.0.dev
Container	Docker version 18.09.7, build 2d0083d fcpindi/c-pac:dev-v1.8 (62e1dcd1fa33) 2021-02-18T10:00:22.916690611Z
System	AWS EC2

Results

In progress, still running despite crashfiles below.

Include:

• Run Command:

cpac -B /media/ebs/CPAC_regtest_pack:/configs /media/ebs/C-PAC/dev/docker_data:/cpac_resources/  \
    --platform docker --tag dev-v1.8 \
    run /media/ebs/runs /media/ebs/runs/2021-02-18/fmriprep-options participant \
    --preconfig fmriprep-options \
    --save_working_dir \
    --data_config_file /configs/data_config_regtest.yml \
    --n_cpus 8 \
    --mem_gb 15

• Pipeline Config
  CPAC/resources/configs/pipeline_config_fmriprep-options.yml
• Data Config
  CPAC_regtest_pack:data_config_regtest.yml

[shnizzedy]

crash-20210218-165631-UID1000-calc_motion_parameters.a0-98680801-26ec-4e40-b4b9-e07cfdc205df.pklz:

Nipype version 1.5.1
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/generate_motion_statistics/generate_motion_statistics.py", line 404, in gen_motion_parameters
    0])  # TODO: mcflirt outputs absdisp, instead of maxdisp

  File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/npyio.py", line 962, in loadtxt
    fh = np.lib._datasource.open(fname, 'rt', encoding=encoding)

  File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/_datasource.py", line 266, in open
    return ds.open(path, mode, encoding=encoding, newline=newline)

  File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/_datasource.py", line 622, in open
    encoding=encoding, newline=newline)

IsADirectoryError: [Errno 21] Is a directory: '/'

working/cpac_1019436/gen_motion_stats_107/_scan_rest_acq-1_run-1/calc_motion_parameters/_report/report.rst:

Node: gen_motion_stats_107 (calc_motion_parameters (interfaces)

Hierarchy : cpac_1019436.gen_motion_stats_107.calc_motion_parameters
Exec ID : calc_motion_parameters.a0

Original Inputs

• function_str : CPAC.generate_motion_statistics.generate_motion_statistics.gen_motion_parameters
• max_displacement : /media/ebs/runs/2021-02-18/fmriprep-options/working/cpac_1019436/_scan_rest_acq-1_run-1/func_motion_correct_mcflirt_90/sub-1019436_ses-1_task-rest_acq-1_run-1_bold_calc_mcf.nii.gz_abs.1D
• motion_correct_tool : mcflirt
• movement_parameters : /media/ebs/runs/2021-02-18/fmriprep-options/working/cpac_1019436/_scan_rest_acq-1_run-1/norm_motion_params_90/motion_params.1D
• scan_id : rest_acq-1_run-1
• subject_id : 1019436

[shnizzedy]

crash-20210218-165631-UID1000-calculate_FDJ.a0-a42eaac0-0437-4702-8697-77d12d7ba9e4.pklz:

Nipype version 1.5.1
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/generate_motion_statistics/generate_motion_statistics.py", line 359, in calculate_FD_J
    rel_rms = np.loadtxt(in_file[1])

  File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/npyio.py", line 962, in loadtxt
    fh = np.lib._datasource.open(fname, 'rt', encoding=encoding)

  File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/_datasource.py", line 266, in open
    return ds.open(path, mode, encoding=encoding, newline=newline)

  File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/_datasource.py", line 624, in open
    raise IOError("%s not found." % path)

OSError: m not found.

working/cpac_1019436/gen_motion_stats_107/_scan_rest_acq-1_run-1/calculate_FDJ/_report:

Node: gen_motion_stats_107 (calculate_FDJ (interfaces)

Hierarchy : cpac_1019436.gen_motion_stats_107.calculate_FDJ
Exec ID : calculate_FDJ.a0

Original Inputs

• function_str : CPAC.generate_motion_statistics.generate_motion_statistics.calculate_FD_J
• in_file : /media/ebs/runs/2021-02-18/fmriprep-options/working/cpac_1019436/_scan_rest_acq-1_run-1/func_motion_correct_mcflirt_90/sub-1019436_ses-1_task-rest_acq-1_run-1_bold_calc_mcf.nii.gz_abs.1D
• motion_correct_tool : mcflirt

[hahaai]

I have the two crash files too on Upenn Cluster using Singularity.
crash-20210218-165631-UID1000-calculate_FDJ.a0-a42eaac0-0437-4702-8697-77d12d7ba9e4.pklz:
crash-20210218-165631-UID1000-calc_motion_parameters.a0-98680801-26ec-4e40-b4b9-e07cfdc205df.pklz: