Workflow did not execute cleanly

[Kwan Chen]

Hi everyone,

I am new to cpac so I'm still learning the ropes. Nonetheless I encountered some errors. Anyone have any suggestions?

The dataset is "ABIDE", which includes 3 subjects with T1 and resting state fmri. All I am hoping to do is process them and view them. Pipeline tests were okay with the subject files.

Anyone have any suggestions on how I should go about interpreting this?

Best,

Kwan






Output:

++ 3dTstat: AFNI version=AFNI_2011_12_21_1014 (Dec 26 2014) [64-bit]
++ Authored by: KR Hammett & RW Cox
++ Output dataset /home/kchen/temp/cpac-abide/working/resting_preproc_session_1/_scan_rest_1_rest/std_dev_0/std_dev.nii.gz
151105-15:08:34,1 workflow INFO:
     [Job finished] jobname: write_log.a0 jobid: 132
151105-15:08:34,4 workflow INFO:
     [Job finished] jobname: std_dev_0.a0 jobid: 133
151105-15:08:34,7 workflow INFO:
     [Job finished] jobname: sinker_38.a0 jobid: 134
151105-15:08:34,10 workflow INFO:
     [Job finished] jobname: func_mask_normalize.a0 jobid: 136
151105-15:08:34,13 workflow INFO:
     [Job finished] jobname: process_outputs_26.a0 jobid: 241
151105-15:08:34,17 workflow INFO:
     [Job finished] jobname: process_outputs_32.a0.a0 jobid: 253
151105-15:08:34,23 workflow INFO:
     Submitting 2 jobs
151105-15:08:34,23 workflow INFO:
     Executing: process_outputs_38.a0 ID: 135
151105-15:08:34,27 workflow INFO:
     Executing: sinker_15.a0 ID: 137
151105-15:08:34,33 workflow INFO:
     Executing node process_outputs_38.a0 in dir: /home/kchen/temp/cpac-abide/working/resting_preproc_session_1/_scan_rest_1_rest/process_outputs_38
151105-15:08:34,34 workflow INFO:
     Executing node sinker_15.a0 in dir: /home/kchen/temp/cpac-abide/working/resting_preproc_session_1/_scan_rest_1_rest/sinker_15
_compcor :  _compcor_None
_csf_threshold :  _csf_threshold_0.96
_gm_threshold :  _gm_threshold_0.7
_target_angle_deg :  _target_angle_deg_90
_threshold :  _threshold_0.2
_wm_threshold :  _wm_threshold_0.96
pipeline :  pipeline_Abide-preprocess
151105-15:08:36,38 workflow INFO:
     [Job finished] jobname: process_outputs_38.a0 jobid: 135
151105-15:08:36,42 workflow INFO:
     [Job finished] jobname: sinker_15.a0 jobid: 137
151105-15:08:36,46 workflow INFO:
     Submitting 1 jobs
151105-15:08:36,46 workflow INFO:
     Executing: process_outputs_15.a0 ID: 138
151105-15:08:36,51 workflow INFO:
     Executing node process_outputs_15.a0 in dir: /home/kchen/temp/cpac-abide/working/resting_preproc_session_1/_scan_rest_1_rest/process_outputs_15
_compcor :  _compcor_None
_csf_threshold :  _csf_threshold_0.96
_gm_threshold :  _gm_threshold_0.7
_target_angle_deg :  _target_angle_deg_90
_threshold :  _threshold_0.2
_wm_threshold :  _wm_threshold_0.96
pipeline :  pipeline_Abide-preprocess
151105-15:08:38,52 workflow INFO:
     [Job finished] jobname: process_outputs_15.a0 jobid: 138
151105-15:08:40,58 workflow INFO:
     ***********************************
151105-15:08:40,58 workflow ERROR:
     could not run node: resting_preproc_session_1.anat_preproc_0.anat_skullstrip
151105-15:08:40,58 workflow INFO:
     crashfile: /home/kchen/temp/cpac-abide/log/crash-20151105-150523-kchen-anat_skullstrip.pklz
151105-15:08:40,59 workflow INFO:
     ***********************************
Process Process-3:
Traceback (most recent call last):
  File "/usr/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
    self.run()
  File "/usr/lib/python2.7/multiprocessing/process.py", line 114, in run
    self._target(*self._args, **self._kwargs)
  File "/usr/local/lib/python2.7/dist-packages/CPAC/pipeline/cpac_pipeline.py", line 5880, in prep_workflow
    workflow.run(plugin='MultiProc', plugin_args={'n_procs': c.numCoresPerSubject})
  File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/engine.py", line 700, in run
    runner.run(execgraph, updatehash=updatehash, config=self.config)
  File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/plugins/base.py", line 268, in run
    report_nodes_not_run(notrun)
  File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/plugins/base.py", line 92, in report_nodes_not_run
    raise RuntimeError(('Workflow did not execute cleanly. '
RuntimeError: Workflow did not execute cleanly. Check log for details

[Cameron Craddock]

Could you type 3dSkullStrip on the command line and see if it give you any errors?

Sent from my iPhone

--
You received this message because you are subscribed to the Google Groups "cpax_forum" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cpax_forum+...@googlegroups.com.
To post to this group, send email to cpax_...@googlegroups.com.
Visit this group at http://groups.google.com/group/cpax_forum.
To view this discussion on the web visit https://groups.google.com/d/msgid/cpax_forum/8924f689-b34d-4033-88c6-6662c9a29802%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Kwan Chen]

3dSkullStrip is installed (if that's what you were trying to figure out).

output:

$ 3dSkullStrip
--     Error 3dSkullStrip (/tmp/buildd/afni-0.20141224~dfsg.1/SUMA/SUMA_3dSkullStrip.c:1312):
Too few parameters. Use 3dSkullStrip for details

Usage: A program to extract the brain from surrounding.
  tissue from MRI T1-weighted images.
  The simplest command would be:
        3dSkullStrip <-input DSET>


When I execute this command:

$ 3dSkullStrip -input mprage.nii.gz

I get two output files with .BRIK and .HEAD.

Just FYI, the AFNI is from neurodebian.

[Cameron Craddock]

Skullstrip requires some libraries that are not always installed. It doesn't look like that is the problem for you. 

Sent from my iPhone

To view this discussion on the web visit https://groups.google.com/d/msgid/cpax_forum/844b031c-3d12-4591-b3ca-33637e93ca2e%40googlegroups.com.

[John Pellman]

Hi Kwan,

Could you send us the crash file located at /home/kchen/temp/cpac-abide/log/crash-20151105-150523-kchen-anat_skullstrip.pklz so that we can take a look at it?

Best,

John Pellman

To view this discussion on the web visit https://groups.google.com/d/msgid/cpax_forum/57EBD62C-C6B9-413E-B751-0B300C873488%40gmail.com.

[John Pellman]

Hi Kwan,

This looks to be an issue with this particular AFNI binary.  Could you run 'apt-get remove afni' and then try installing the latest AFNI binary using the instructions in the link below?

http://afni.nimh.nih.gov/pub/dist/HOWTO/howto/ht00_inst/html/linux_inst_basic.html

Best,

John Pellman

[Kwan Chen]

Sure I'll give that a try and let you know what happens.

You received this message because you are subscribed to a topic in the Google Groups "cpax_forum" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/cpax_forum/4vnlcBhuAvc/unsubscribe.
To unsubscribe from this group and all its topics, send an email to cpax_forum+...@googlegroups.com.

To post to this group, send email to cpax_...@googlegroups.com.
Visit this group at http://groups.google.com/group/cpax_forum.

To view this discussion on the web visit https://groups.google.com/d/msgid/cpax_forum/CANtQzOHmv%2BFnA9yKNX5gnodLaHnZSz2rH%3DoGjCBXYxXsVynRog%40mail.gmail.com.

[John Pellman]

For future reference for anyone who encounters a similar issue, we determined that the AFNI binary was the source of the problem.  The error that the version of 3dSkullstrip (distributed with Neurodebian) was "freeglut (3dSkullStrip): failed to open display ':1'".  Therefore, if the Neurodebian AFNI binary does not work, downloading a compiled version of AFNI from the AFNI website would be the next thing to try.

To view this discussion on the web visit https://groups.google.com/d/msgid/cpax_forum/CAHHUaUQ%3DfS5AM3xi--Zj19%2BPH5Byw9mqtRD4VgVhq%3DD4DSnUsw%40mail.gmail.com.