[Neurodebian-devel] Fwd: [cpax_forum] Workflow did not execute cleanly
John Pellman
pellman.john at gmail.com
Fri Nov 20 14:57:11 UTC 2015
Hi,
I just wanted to forward this exchange we recently had on the support forum
for our neuroimaging package C-PAC (which uses AFNI via Nipype). It looks
like the AFNI binary in Neurodebian is currently broken.
--John Pellman
---------- Forwarded message ----------
From: John Pellman <pellman.john at gmail.com>
Date: 2015-11-20 9:52 GMT-05:00
Subject: Re: [cpax_forum] Workflow did not execute cleanly
To: cpax_forum at googlegroups.com
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.
2015-11-06 15:22 GMT-05:00 Kwan Chen <kwan.chen at gmail.com>:
> Sure I'll give that a try and let you know what happens.
>
> On Fri, Nov 6, 2015, 3:21 PM John Pellman <pellman.john at gmail.com> wrote:
>
>> 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
>>
>> 2015-11-06 14:22 GMT-05:00 John Pellman <pellman.john at gmail.com>:
>>
>>> 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
>>>
>>> 2015-11-06 14:22 GMT-05:00 Cameron Craddock <cameron.craddock at gmail.com>
>>> :
>>>
>>>> Skullstrip requires some libraries that are not always installed. It
>>>> doesn't look like that is the problem for you.
>>>>
>>>> Sent from my iPhone
>>>>
>>>> On Nov 6, 2015, at 2:17 PM, Kwan Chen <kwan.chen at gmail.com> wrote:
>>>>
>>>> 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.
>>>> On Friday, November 6, 2015 at 9:01:21 AM UTC-5, Cameron Craddock wrote:
>>>>>
>>>>> Could you type 3dSkullStrip on the command line and see if it give you
>>>>> any errors?
>>>>>
>>>>> Sent from my iPhone
>>>>>
>>>>> On Nov 6, 2015, at 8:57 AM, Kwan Chen <kwan... at gmail.com> wrote:
>>>>>
>>>>> 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
>>>>>
>>>>>
>>>>>
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