Dear neurodebian users and developers,
I am using condor for bedpostx paralelising on Ubuntu 12.04. The
computation worked but suddenly it does not. Does anyone have same
problem? Some problem with update or something else?
Here is my folder with dMRI data. I think everything should be right.
labounek@PC-E229-455:/media/407285B97285B3E6/Data/humanconnectome/Q3/151526/T1w/Diffusion$
*ls**
*bedpostx_qsub.RZG87UQEgeo23* bvals bvecs data.nii.gz
grad_dev.nii.gz nodif_brain_mask.nii.gz**
*
Now, when I will use bedpostx comand with default parameter setting I
will get the condor output:
*fsl5.0-bedpostx
/media/407285B97285B3E6/Data/humanconnectome/Q3/151526/T1w/Diffusion*
______________________________________________________________________________________________________________________________________
subjectdir is
/media/407285B97285B3E6/Data/humanconnectome/Q3/151526/T1w/Diffusion
Making bedpostx directory structure
Queuing preprocessing stages
Queuing parallel processing stage
Queuing post processing stage
Type
/media/407285B97285B3E6/Data/humanconnectome/Q3/151526/T1w/Diffusion.bedpostX/monitor
to show progress.
Type
/media/407285B97285B3E6/Data/humanconnectome/Q3/151526/T1w/Diffusion.bedpostX/cancel
to terminate all the queued tasks.
You will get an email at the end of the post-processing stage.
______________________________________________________________________________________________________________________________________
The Diffusion.bedpostx folder is created including tipical folders and
files.
labounek@PC-E229-455:/media/407285B97285B3E6/Data/humanconnectome/Q2/Q2_diffusion_preprocessed/499566/T1w/Diffusion.bedpostX$
*ls**
**cancel commands.txt diff_slices logs monitor xfms*
After comand:
*/media/407285B97285B3E6/Data/humanconnectome/Q3/151526/T1w/Diffusion.bedpostX/monitor
*; I will get lots error messages lokking like these shown below and the
calculation is not working.
__________________________________________________________________________________________________________________________________________________
/media/407285B97285B3E6/Data/humanconnectome/Q3/151526/T1w/Diffusion.bedpostX/monitor:
1:
/media/407285B97285B3E6/Data/humanconnectome/Q3/151526/T1w/Diffusion.bedpostX/monitor:
/bin/zeropad: not found
/media/407285B97285B3E6/Data/humanconnectome/Q3/151526/T1w/Diffusion.bedpostX/monitor:
1:
/media/407285B97285B3E6/Data/humanconnectome/Q3/151526/T1w/Diffusion.bedpostX/monitor:
/bin/imtest: not found
/media/407285B97285B3E6/Data/humanconnectome/Q3/151526/T1w/Diffusion.bedpostX/monitor:
10: [: -eq: unexpected operator
__________________________________________________________________________________________________________________________________________________
In error, there is writen /bin/zeropad: not found and /bin/imtest: not
found. I am not sure what this files should do but truly I have not them
on hard disk.
Preprocessing, processing and postprocessing did not start. I have no
idea what to do.
Best,
Rene
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