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bids-apps / CPAC

BIDS Application for the Configurable Pipeline for the Analysis of Connectomes (C-PAC)
Apache License 2.0
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CPAC crashes before completion #31

Open araikes opened 6 years ago

araikes commented 6 years ago

Greetings, I have been running the BIDS-App CPAC docker container image (v1.0.2_disable_log_2) on test participants in two different datasets. CPAC crashes out prior to completion.

The crash error in the pypeline.log file reads:

180330-02:24:47,161 workflow ERROR: could not run node: resting_preproc_sub-166_ses-1.gen_motion_stats_0.calc_spike_percent.a0.c0 180330-02:24:47,162 workflow INFO: crashfile: /outputs/crash/crash-20180330-002347-root-calc_spike_percent.a0.c0-8b8c1d4c-4aef-4ba6-a40a-a4b7996d54f7.pklz 180330-02:24:47,163 workflow INFO:

I'm uploading the full pypeline.log file and can send the crash log .pklz file if needed.

Thanks pypeline.log

ccraddock commented 6 years ago

Sorry for the late reply.

here is the error in your log file:

File "/usr/local/bin/miniconda/lib/python2.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 52, in run_node result['result'] = node.run(updatehash=updatehash) File "/usr/local/bin/miniconda/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 372, in run self._run_interface() File "/usr/local/bin/miniconda/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 482, in _run_interface self._result = self._run_command(execute) File "/usr/local/bin/miniconda/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 613, in _run_command result = self._interface.run() File "/usr/local/bin/miniconda/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1081, in run runtime = self._run_wrapper(runtime) File "/usr/local/bin/miniconda/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1029, in _run_wrapper runtime = self._run_interface(runtime) File "/usr/local/bin/miniconda/lib/python2.7/site-packages/nipype/interfaces/utility/wrappers.py", line 194, in _run_interface out = function_handle(**args) File "", line 17, in calc_percent Exception: A string was entered for the de-spiking/scrubbing threshold, but there is no percent value. Interface Function failed to run.

Looks like the scrubbing threshold was set to the wrong value. @sgiavasis would you please give the correct value for this?

sgiavasis commented 6 years ago

Hi @araikes,

Are you running a default pipeline, or a modified pipeline config? If a modified one-Not sure if you have scrubbing enabled, but either way, try entering some typical float value (such as 0.2) into the brackets, without quotes, in the spikeThreshold pipeline option and see if you still get that error.

Also, a much newer version of the C-PAC container (v1.1.0) is available- I would recommend trying that one instead.

Best, Steve

araikes commented 6 years ago

Hi @sgiavasis, I'm running the default pipeline. When I pulled the docker image, the older version is what I got. Is there a specific location for v 1.1.0?

araikes commented 6 years ago

@sgiavasis and @ccraddock, I have successfully updated to version 1.1.0 and finally have a moment to try using this Docker image again. However, I'm running into the following issue:

My data set is BIDS compliant with the structure: bids_dataset/sub-/ Whenever I run the test_config or attempt to use the pipeline, I receive an error that no anatomical images were found at: bids_dataset//sub-/ses-/sub-_ses-*_T1w.nii.

Is there a way to compel CPAC's docker not to look for a site folder? I've tried running the GUI to no avail and do not presently have singularity available to me.

sgiavasis commented 5 years ago

Hi @araikes,

There is a way to bypass the BIDS validator by supplying the --skip_bids_validator flag at the end of your docker run command, but I'm curious as to why this issue is popping up in the first place.

Can you paste the exact error message you get?

Thanks! Steve