structural-pipeline-measures fails（ with docker image）

feifei6699 commented 3 years ago

Hello, I have successfully run the dhcp-structural-pipeline with the docker image. However, when I tried to run the structural-pipeline-measures with the docker image using the command: "sudo docker run --rm -t -v $PWD/data:/data -u $(id -u):$(id -g) biomedia/dhcp-structural-pipeline-measures:latest /data/participants.tsv --reporting" the error occurred

**feifei@feifei-virtual-machine:/var/lib/docker$ sudo docker run --rm -t -v $PWD/data:/data -u $(id -u):$(id -g) biomedia/dhcp-structural-pipeline-measures:latest /data/participants.tsv --reporting Reporting for the dHCP pipeline

Derivatives directory: /data/derivatives participants.tsv: /data/participants.tsv datadir: /data scriptdir: /usr/src/structural-pipeline-measures/scripts reportsdir: /data/reports logdir: /data/logs reporting: 1

/usr/src/structural-pipeline-measures/pipeline.sh /data/participants.tsv --reporting

CC00060XX03 bad gender 12501 computing volume/surface measurements of subjects... gathering volume/surface measurements of subjects... completed volume/surface measurements

computing QC measurements for subjects...

gathering QC measurements of subjects... creating QC reports... structural_dhcp_mriqc -o /data/reports -w /data/reports/workdir --dhcp-measures /data/reports/dhcp-measurements.json --qc-measures /data/reports/qc-measurements.json --nthreads 1 failed**

The "qc.err" file: Traceback (most recent call last): File "/usr/local/bin/structural_dhcp_mriqc", line 11, in sys.exit(main()) File "/usr/local/lib/python3.5/dist-packages/structural_dhcp_mriqc/utils/mriqc_run.py", line 144, in main run_id=opts.run_id, settings=settings) File "/usr/local/lib/python3.5/dist-packages/structural_dhcp_mriqc/workflows/core.py", line 37, in ms_anat_dhcp with open(settings['qc_measures'], 'r') as jsondata: FileNotFoundError: [Errno 2] No such file or directory: '/data/reports/qc-measurements.json' Traceback (most recent call last): File "/usr/local/bin/structural_dhcp_mriqc", line 11, in sys.exit(main()) File "/usr/local/lib/python3.5/dist-packages/structural_dhcp_mriqc/utils/mriqc_run.py", line 144, in main run_id=opts.run_id, settings=settings) File "/usr/local/lib/python3.5/dist-packages/structural_dhcp_mriqc/workflows/core.py", line 49, in ms_anat_dhcp raise RuntimeError('No scans found in %s' % settings['dhcp_data']) KeyError: 'dhcp_data'

How to deal with this problem?

Thanks in advance

Thea-Eddie-Amy commented 3 years ago

@feifei6699 Hi, have you solved the problem? I met the same situation as you did. Please let me know if you made some progress. Thanks!

feifei6699 commented 3 years ago

@feifei6699 Hi, have you solved the problem? I met the same situation as you did. Please let me know if you made some progress. Thanks!

Hi, I have solved the problem as followed,

    The "participants.tsv" should have lines like:

    participant_id  gender  birth_ga
    CC001              Female   44.0
    CC002              Male       42.0
     etc.

    There should not be a session number.

Hope it will help you!

Thea-Eddie-Amy commented 3 years ago

@feifei6699 Hi, have you solved the problem? I met the same situation as you did. Please let me know if you made some progress. Thanks!

Hi, I have solved the problem as followed,
    The "participants.tsv" should have lines like:

    participant_id  gender  birth_ga
    CC001              Female   44.0
    CC002              Male       42.0
     etc.

    There should not be a session number.
Hope it will help you!

Thank you so much!! I managed to run the measure pipeline where I get all the results in workdir, however met some problems with QC reporting. Here is the log&error: *********************************** 210313-02:56:23,564 workflow ERROR: could not run node: anatMRIQC.MRIQC_Anat.plot_mosaic.a0 210313-02:56:23,565 workflow INFO: crashfile: /30_0_liuwenting/reports/workdir_log/crash-20210313-025620-root-plot_mosaic.a0-89e57ee6-6105-4ff3-bc2c-7cc38a6fdd03.pklz 210313-02:56:23,565 workflow INFO: ***********************************

Traceback (most recent call last): File "/usr/local/bin/structural_dhcp_mriqc", line 11, in <module> sys.exit(main()) File "/usr/local/lib/python3.5/dist-packages/structural_dhcp_mriqc/utils/mriqc_run.py", line 146, in main workflow.run(**plugin_settings) File "/usr/local/lib/python3.5/dist-packages/nipype/pipeline/engine/workflows.py", line 595, in run runner.run(execgraph, updatehash=updatehash, config=self.config) File "/usr/local/lib/python3.5/dist-packages/nipype/pipeline/plugins/linear.py", line 61, in run report_nodes_not_run(notrun) File "/usr/local/lib/python3.5/dist-packages/nipype/pipeline/plugins/tools.py", line 81, in report_nodes_not_run raise RuntimeError(('Workflow did not execute cleanly. ' RuntimeError: Workflow did not execute cleanly. Check log for details

I have no idea where went wrong, please help. Thanks!

feifei6699 commented 3 years ago

@feifei6699 Hi, have you solved the problem? I met the same situation as you did. Please let me know if you made some progress. Thanks!

Hi, I have solved the problem as followed,
    The "participants.tsv" should have lines like:

    participant_id  gender  birth_ga
    CC001              Female   44.0
    CC002              Male       42.0
     etc.

    There should not be a session number.
Hope it will help you!
Thank you so much!! I managed to run the measure pipeline where I get all the results in workdir, however met some problems with QC reporting. Here is the log&error: *********************************** 210313-02:56:23,564 workflow ERROR: could not run node: anatMRIQC.MRIQC_Anat.plot_mosaic.a0 210313-02:56:23,565 workflow INFO: crashfile: /30_0_liuwenting/reports/workdir_log/crash-20210313-025620-root-plot_mosaic.a0-89e57ee6-6105-4ff3-bc2c-7cc38a6fdd03.pklz 210313-02:56:23,565 workflow INFO: ***********************************

Traceback (most recent call last): File "/usr/local/bin/structural_dhcp_mriqc", line 11, in <module> sys.exit(main()) File "/usr/local/lib/python3.5/dist-packages/structural_dhcp_mriqc/utils/mriqc_run.py", line 146, in main workflow.run(**plugin_settings) File "/usr/local/lib/python3.5/dist-packages/nipype/pipeline/engine/workflows.py", line 595, in run runner.run(execgraph, updatehash=updatehash, config=self.config) File "/usr/local/lib/python3.5/dist-packages/nipype/pipeline/plugins/linear.py", line 61, in run report_nodes_not_run(notrun) File "/usr/local/lib/python3.5/dist-packages/nipype/pipeline/plugins/tools.py", line 81, in report_nodes_not_run raise RuntimeError(('Workflow did not execute cleanly. ' RuntimeError: Workflow did not execute cleanly. Check log for details

I have no idea where went wrong, please help. Thanks!

I met the same problem, I had no idea too.

amakropoulos / structural-pipeline-measures

structural-pipeline-measures fails（ with docker image） #5

/usr/src/structural-pipeline-measures/pipeline.sh /data/participants.tsv --reporting

CC00060XX03 bad gender 12501 computing volume/surface measurements of subjects... gathering volume/surface measurements of subjects... completed volume/surface measurements