Trouble processing ABIDE II data (ndmg mode)

[eigenvivek]

I am trying to use the latest Docker image for C-PAC to process MRI scans from the Autism Brain Imaging Data Exchange II (ABIDE II). I want to use the ndmg configuration to generate the connectomes, but am encountering errors that I don't know how to resolve. Any and all help is greatly appreciated :)

Setting up the pipeline

1. The ABIDE II data is not natively in the BIDS format, so I reformatted my files to look like this:

2. I found a config file for using C-PAC in ndmg mode here in your resources folder. I downloaded it to my local directory.

3. I then pulled the latest Docker Image for C-PAC with docker pull fcpindi/c-pac:latest and started the pipeline with this command:

   docker run -i --rm \
   -v <input_filepath>:/bids_dataset \
   -v <output_filepath>:/outputs \
   -v <config_filepath>:/configs \
   fcpindi/c-pac:latest /bids_dataset /outputs participant \
   --pipeline_file configs/ndmg.yml

Output

C-PAC runs for about 30 minutes and then returns this error message

190613-13:25:28,401 nipype.workflow INFO:

    Error of subject workflow resting_preproc_sub-30229_ses-1

    CPAC run error:

        Pipeline configuration: analysis_ndmg
        Subject workflow: resting_preproc_sub-30229_ses-1
        Elapsed run time (minutes): 30.2007092516
        Timing information saved in /outputs/log/cpac_individual_timing_analysis_ndmg.csv
        System time of start:      2019-06-13 12:55:19

190613-13:25:28,403 nipype.workflow INFO:
     Removing working dir: /tmp/resting_preproc_sub-30229_ses-1

I have the latest crash log saved on my computer, but I don't know how to read the .pklz file.

[sgiavasis]

Hi @v715,

You can read the Nipype crash files using: nipypecli crash <path to crash file.pklz>

Is there anything in the output stream or log file just before the end of the pipeline that mentions anything about an error or crash? Or, what the last thing was before it ended?

Steve

[sgiavasis]

Hi @v715 ,

Not sure if you've given this another try, but we just released C-PAC version 1.6.2, and this includes a fix for a bug some users were seeing with the ndmg-f preconfigured pipeline.

Try re-pulling fcpindi/c-pac:latest and see if you still get a crash.

Best, Steve

[sgiavasis]

Closing due to inactivity- please feel free to reopen if you are still having issues.