crash with multisession BIDS data

[yonestar]

Hi Tamas,

It is wonderful that you made this great tool, AND, that you made it so accessible w/ a docker. I am excited to be applying it to my data.

The docker is crashing for me. The logs are attached. I tried it on two subjects, one with --keep-derivatives and one without. The error messages seem a bit different. Attaching the logs now.
Archive.zip

Both subjects are in valid BIDS format.

I have one guess as to a potential problem. I have data from multiple time points (pre- and post-treatment), so my bids structure is subject/ses-XX/anat,func,fmap. Perhaps your code does not expect the session level? Also, my data is all gzipped

Thanks
Yoni Ashar
Wager lab

[spisakt]

Hi Yoni,

Sorry for the late replay!
Indeed, the app wasn't tested with session level.

On the other hand, it uses nipype's BIDSDataGrabber(), so should theoretically be able to handle it.

The error message says that no T1w file was found.
Is your anatomical image named like "anat/sub-XXX-T1w.nii.gz"? Do you have the "T1w" tag there?
(Gzipped data must work without any problem)

Thanks
Tamas

[yonestar]

Hi Tamas, I have a structural image for each session (in my case, two sessions). So it is: <bids folder>/<subject>/<ses-XX>/anat/sub-XXXX_ses-X_T1w.nii.gz I do NOT have any sub-XXX/anat folder, that is not nested under a session. Maybe that is it?? thank you! Yoni

…

On Tue, Apr 7, 2020 at 6:04 AM Tamas Spisak ***@***.***> wrote: Hi Yoni, Sorry for the late replay! Indeed, the app wasn't tested with session level. On the other hand, it uses nipype's BIDSDataGrabber(), so should theoretically be able to handle it. The error message says that no T1w file was found. Is your anatomical image named like "anat/sub-XXX-T1w.nii.gz"? Do you have the "T1w" tag there? (Gzipped data must work without any problem) Thanks Tamas — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#5 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABCOBDRY2IRZ76JSLZECX43RLL3BLANCNFSM4LTCGRAA> .

[granitz]

I have a similar issue. Although data is in /sub-XXX/anat folder. Unfortunately I cannot find the crash file in tmp folder.

crashfile: /tmp/crash-20200414-073808-root-_reorient_func2-10753938-0f5d-4d7b-8519-240e8919e468.pklz
            200414-11:03:19,727 nipype.workflow INFO:
  	 ***********************************
  Traceback (most recent call last):
    File "/home/rpn-signature/src/RPN-signature/pipeline/rpn-signature.py", line 366, in <module>
      totalWorkflow.run(plugin='MultiProc', plugin_args=plugin_args)
    File "/usr/local/miniconda/lib/python2.7/site-packages/nipype/pipeline/engine/workflows.py", line 599, in run
      runner.run(execgraph, updatehash=updatehash, config=self.config)
    File "/usr/local/miniconda/lib/python2.7/site-packages/nipype/pipeline/plugins/base.py", line 191, in run
      report_nodes_not_run(notrun)
    File "/usr/local/miniconda/lib/python2.7/site-packages/nipype/pipeline/plugins/tools.py", line 82, in report_nodes_not_run
      raise RuntimeError(('Workflow did not execute cleanly. '
  RuntimeError: Workflow did not execute cleanly. Check log for details

[spisakt]

Hi everyone,
Thanks for the feedback and apologies again for the late response.

@granitz: It's not clear if it is the same bug. Can you find the crash file in the folder where the output is?
Or is there a line like this in your script output:

raise IOError(msg)
IOError: Output key: T1w returned no files

@yonestar: I had a brief look and it seems like it's an issue of the nipype version inside the docker container. Simply said: The problem is relatively simply to resolve, but I have to redo all the packaging and fight potential dependency problems.
Unfortunately, i am quite busy right now and can't do this with a short deadline.

A workaround could be that you "flatten" your BIDS structure, that is, you pretend that you have single session data (by treating sessions as subjects or - even better - by having two separate BIDS folders, one for the pre and one for the post).

Is it an option for you, or you rather wait for the fix?

Cheers,
Tamas

[granitz]

Hi everyone,
Thanks for the feedback and apologies again for the late response.

@granitz: It's not clear if it is the same bug. Can you find the crash file in the folder where the output is?
Or is there a line like this in your script output:

raise IOError(msg)
IOError: Output key: T1w returned no files

@yonestar: I had a brief look and it seems like it's an issue of the nipype version inside the docker container. Simply said: The problem is relatively simply to resolve, but I have to redo all the packaging and fight potential dependency problems.
Unfortunately, i am quite busy right now and can't do this with a short deadline.

A workaround could be that you "flatten" your BIDS structure, that is, you pretend that you have single session data (by treating sessions as subjects or - even better - by having two separate BIDS folders, one for the pre and one for the post).

Is it an option for you, or you rather wait for the fix?

Cheers,
Tamas

Thank you for your response. The problem of finding the crash file persists. And I'm not getting this error: IOError: Output key: T1w returned no files. These are the last few lines, although I'm not sure if this helps.

200418-19:44:31,131 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 6.80/7.00, Free processors: 3/4.
Currently running:
* RPN.func2anat.vent_bb_mask
200418-19:45:08,714 nipype.workflow INFO:
[Node] Finished "_vent_bb_mask0".
200418-19:45:08,722 nipype.workflow INFO:
[Node] Finished "RPN.func2anat.vent_bb_mask".
200418-19:45:09,139 nipype.workflow INFO:
[Job 108] Completed (RPN.func2anat.vent_bb_mask).
200418-19:45:09,147 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 0 jobs ready. Free memory (GB): 7.00/7.00, Free processors: 4/4.
200418-19:45:11,139 nipype.workflow INFO:
***********************************
200418-19:45:11,140 nipype.workflow ERROR:
could not run node: RPN.reorient_func
200418-19:45:11,141 nipype.workflow INFO:
crashfile: /tmp/crash-20200418-160355-root-_reorient_func0-137cec49-cb41-45ef-a303-ec279108e700.pklz
200418-19:45:11,142 nipype.workflow ERROR:
could not run node: RPN.reorient_func
200418-19:45:11,144 nipype.workflow INFO:
crashfile: /tmp/crash-20200418-160357-root-_reorient_func2-698e3ea4-1aec-4be2-b569-0883b2d64f7b.pklz
200418-19:45:11,145 nipype.workflow INFO:
***********************************
Traceback (most recent call last):
File "/home/rpn-signature/src/RPN-signature/pipeline/rpn-signature.py", line 366, in
totalWorkflow.run(plugin='MultiProc', plugin_args=plugin_args)
File "/usr/local/miniconda/lib/python2.7/site-packages/nipype/pipeline/engine/workflows.py", line 599, in run
runner.run(execgraph, updatehash=updatehash, config=self.config)
File "/usr/local/miniconda/lib/python2.7/site-packages/nipype/pipeline/plugins/base.py", line 191, in run
report_nodes_not_run(notrun)
File "/usr/local/miniconda/lib/python2.7/site-packages/nipype/pipeline/plugins/tools.py", line 82, in report_nodes_not_run
raise RuntimeError(('Workflow did not execute cleanly. '
RuntimeError: Workflow did not execute cleanly. Check log for details

[spisakt]

Can you find the crash file, when specifying the --debug option?
That will save all temporary files in the output directory.