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FCP-INDI / cpac_run_logs

Repository for information about C-PAC runs.
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C-PAC v1.8.0.dev - preproc preconfig #14

Open shnizzedy opened 3 years ago

shnizzedy commented 3 years ago

C-PAC Run Info
Description preproc 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

The run completes!

    CPAC run complete:

        Pipeline configuration: cpac_preproc
        Subject workflow: cpac_0010042
        Elapsed run time (minutes): 25.424772437413534
        Timing information saved in /media/ebs/runs/2021-02-18/preproc/log/cpac_individual_timing_cpac_preproc.csv
        System time of start:      2021-02-18 20:31:01
        System time of completion: 2021-02-18 20:56:26

Each completed subject's out/**/qc directory just contains a single file like

qc
└── index.html

qc/index.html

so something seems not right with QC…

Include:

cpac -B /media/ebs/CPAC_regtest_pack:/configs /media/ebs/C-PAC:/code /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/preproc participant \
    --preconfig preproc \
    --save_working_dir \
    --data_config_file /configs/data_config_regtest.yml \
    --n_cpus 8 \
    --mem_gb 15
shnizzedy commented 3 years ago

Also one subject had 2 crashfiles, but I'm pretty sure that's (data + config)-specific:

crash-20210218-203058-UID1000-build_nuisance_regressors.a0-a7e5cd81-647e-4e53-8840-afaee75cde44.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/nuisance/nuisance.py", line 197, in gather_nuisance
    regressor_length))

ValueError: Number of time points in /media/ebs/runs/2021-02-18/preproc/working/cpac_7774305/nuisance_regressors_Regressor-1_135/_scan_rest_acq-1_run-1/CerebrospinalFluid_mean/sub-7774305_ses-1_task-rest_acq-1_run-1_bold_calc_tshift_resample_flirt_roistat.1D (0) is inconsistent with length of functional file /media/ebs/runs/2021-02-18/preproc/working/cpac_7774305/_scan_rest_acq-1_run-1/func_reorient_78/sub-7774305_ses-1_task-rest_acq-1_run-1_bold_calc_tshift_resample.nii.gz (152)

crash-20210218-203052-UID1000-build_nuisance_regressors.a0-f40a904c-3f69-43e7-ac2e-05c3e0d908ee.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/nuisance/nuisance.py", line 197, in gather_nuisance
    regressor_length))

ValueError: Number of time points in /media/ebs/runs/2021-02-18/preproc/working/cpac_7774305/nuisance_regressors_Regressor-2_135/_scan_rest_acq-1_run-1/CerebrospinalFluid_mean/sub-7774305_ses-1_task-rest_acq-1_run-1_bold_calc_tshift_resample_flirt_roistat.1D (0) is inconsistent with length of functional file /media/ebs/runs/2021-02-18/preproc/working/cpac_7774305/_scan_rest_acq-1_run-1/func_reorient_78/sub-7774305_ses-1_task-rest_acq-1_run-1_bold_calc_tshift_resample.nii.gz (152)

(like https://github.com/FCP-INDI/cpac_run_logs/issues/9#issuecomment-781572993)