[log in to unmask]" type="cite">

Hi René,

.bash_profile doesn't exist initially.

I see that you are running fsl using "fsl5.0-".

Could you please execute these two commands:

echo ". /etc/fsl/5.0/fsl.sh" >> ~/.bashrc

echo "if [ -f ~/.bashrc ]; then . ~/.bashrc; fi" >> ~/.bash_profile

It will add in the first command the settings to your interactive terminals and in the second anything you have .bashrc to your remote login shells (which are used by other softwares as well).

After that, try the experiment again in a new terminal.

Cheers,

Alex

Alexandre Manhães Savio <[log in to unmask]>
Grupo de Inteligencia Computacional
Departamento de CCIA
UPV/EHU

On 4 December 2013 16:53, René Labounek <[log in to unmask]> wrote:

Helo Alex,
I did not set any of these .bash files before. I have added neurodebian to my repositary and installed fsl. Then I have started to use bedpostx function but it worked only on one processor. I have found this instructions about paralelising with condor and installed condor.

http://neuro.debian.net/blog/2012/2012-03-09_parallelize_fsl_with_condor.html

In /etc/fsl/fsl.sh, I have changed: export FSLPARALLEL=condor. The calculation was working on all my processors. Since that time, I have not changed anything. Today, I wanted to start new calculation and it is not working.

I was looking into all files you have written but nowhere I did not find any variable called FSL or something like that. Maybe problem is here but I do not know which variables I should define. If I understand these files serves for definition of global bash variables. On my PC, I have found .bashrc and /etc/bash.bashrc, not found ~/.bash_profile.

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.

Even, I am not sure I should write this problem here or on some neurodebian forum.

Rene


Dne 4.12.2013 16:03, [log in to unmask] napsal(a):

Hello René,

Have you set your ~/.bash_profile file?

It should source either your fsl settings or your .bashrc or /etc/bash.bashrc file if you have them changed for FSL.

If that is the case, more info here:
http://mywiki.wooledge.org/DotFiles

I hope this helps.

Cheers,
Alex

Alexandre Manhães Savio <[log in to unmask]>
Grupo de Inteligencia Computacional
Departamento de CCIA
UPV/EHU

On 4 December 2013 15:50, René Labounek <[log in to unmask]> wrote:

Dear FSL users,

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
__________________________________________________________________________________________________________________________________________________

Preprocessing, processing and postprocessing did not start. I have no idea what to do.

Best,
Rene