recon-all command not running as a node

[Shahrzad KHM]

Hi
I have a basic problem running my frist nipype code.
recon-all as a node in a workflow (attached to the datagraber node) does not run but when I coppied the command from the workflow directory to shell it works properly (means that inputs and outputs were correct). What could cause this issue?
The Error of the Workflow is as following:
Running: recon-all -all -i /MYDISK/project/2014_analysis/freesurfer/subjest01/anat/MPRAGE_RPI.nii -subjid subjest01 -sd /MYDISK/project/2014_analysis//freesurfer/subjects
140416-00:54:52,76 workflow ERROR:
['Node recon_all.a0 failed to run on host .']
Thanks a lot
S.

[Chris Filo Gorgolewski]

Hi Shahrzad,

Did the workflow produce a crash file? You can view it using the nipype_display_crash command to see what exactly went wrong.

My best guess is that the environment was not set up correctly (as in all the freesurfer environmental variables - just type "freesurfer" in the terminal you run your pipelines 1)

Best,

Chris

1 This is an MPI CBS specific script.

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[Shahrzad KHM]

True, Thanks :)

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[Shahrzad KHM]

Hi again, Now I have another problem.

The Crash file says that the recon-all is already running and I have to remove a file if I insist to run it again. I removed it and re-ran the program but again the program crashes.

And here is the crash file:

File: crash-20140416-151142-kharabian-recon_all.a0.npz
Node: main_workflow.recon_all.a0
Working directory: /scr/somalia3/life/2014_analysis/freesurfer/working/preprecossing/main_workflow/_subject_id_LI00000031/recon_all


Node inputs:

T1_files = ['/scr/somalia3/life/2014_analysis/freesurfer/LI00000031/anat/MPRAGE_RPI.nii']
T2_file = <undefined>
args = <undefined>
directive = all
environ = {}
flags = <undefined>
hemi = <undefined>
ignore_exception = False
openmp = <undefined>
subject_id = LI00000031
subjects_dir = /scr/somalia3/life/2014_analysis/freesurfer/subjects
terminal_output = stream



Traceback:
Traceback (most recent call last):
  File "/scr/somalia3/life/2014_analysis/freesurfer/working/preprecossing/main_workflow/batch/pyscript_20140416_124356_main_workflow_recon_all.a0.py", line 26, in <module>
    result = info['node'].run(updatehash=info['updatehash'])
  File "/usr/lib/pymodules/python2.7/nipype/pipeline/engine.py", line 1386, in run
    self._run_interface()
  File "/usr/lib/pymodules/python2.7/nipype/pipeline/engine.py", line 1496, in _run_interface
    self._result = self._run_command(execute)
  File "/usr/lib/pymodules/python2.7/nipype/pipeline/engine.py", line 1622, in _run_command
    result = self._interface.run()
  File "/usr/lib/pymodules/python2.7/nipype/interfaces/base.py", line 946, in run
    runtime = self._run_interface(runtime)
  File "/usr/lib/pymodules/python2.7/nipype/interfaces/base.py", line 1383, in _run_interface
    self.raise_exception(runtime)
  File "/usr/lib/pymodules/python2.7/nipype/interfaces/base.py", line 1313, in raise_exception
    raise RuntimeError(message)
RuntimeError: Command:
recon-all -autorecon2  -subjid LI00000031 -sd /scr/somalia3/life/2014_analysis/freesurfer/subjects -nomotioncor -notalairach -nonuintensitycor -nonormalization -noskullstrip -nogcareg -nocanorm -careg -careginv -rmneck -skull-lta -calabel -normalization2 -maskbfs -segmentation -fill -tessellate -smooth1 -inflate1 -qsphere -fix -white -smooth2 -inflate2 -sphere -surfreg -jacobian_white -avgcurv -cortparc -pial -cortparc2 -parcstats2 -cortribbon -segstats -aparc2aseg -wmparc -balabels -label-exvivo-ec
Standard output:

WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!

Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /scr/somalia3/life/2014_analysis/freesurfer/subjects
Actual FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/5.3.0/amd64/_all
-rw-rw-r-- 1 kharabian users 149983 Apr 16 15:06 /scr/somalia3/life/2014_analysis/freesurfer/subjects/LI00000031/scripts/recon-all.log
Linux miller 3.2.0-61-generic #92-Ubuntu SMP Mon Mar 31 23:47:59 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux

ERROR: it appears that recon-all is already running
for LI00000031 based on the presence of /scr/somalia3/life/2014_analysis/freesurfer/subjects/LI00000031/scripts/IsRunning.lh+rh. It could
also be that recon-all was running at one point but
died in an unexpected way. If it is the case that there
is a process running, you can kill it and start over or
just let it run. If the process has died, you should type:

rm /scr/somalia3/life/2014_analysis/freesurfer/subjects/LI00000031/scripts/IsRunning.lh+rh

and re-run. Or you can add -no-isrunning to the recon-all
command-line. The contents of this file are:
----------------------------------------------------------
------------------------------
SUBJECT LI00000031
HEMI    lh rh
DATE Wed Apr 16 12:52:02 CEST 2014
USER kharabian
HOST adenauer
PROCESSID 19303
PROCESSOR x86_64
OS Linux
Linux adenauer 3.2.0-61-generic #92-Ubuntu SMP Mon Mar 31 23:47:59 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
----------------------------------------------------------
Standard error:

Return code: 1
Interface ReconAll failed to run.

Can you help me with this issue?

Bests,

S.

[Chris Filo Gorgolewski]

On Wed, Apr 16, 2014 at 3:44 PM, Shahrzad KHM <shahr...@gmail.com> wrote:

/scr/somalia3/life/2014_analysis/freesurfer/subjects/LI00000031/scripts/IsRunning.lh+rh

are you sure: /scr/somalia3/life/2014_analysis/freesurfer/subjects/LI00000031/scripts/IsRunning.lh+rh was removed?

[Shahrzad KHM]

yes, I did it before running the script again.