[Neurodebian-users] bedpostx with condor is not working

[René Labounek]

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 at 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 at 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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