Hi,

Apparently PANDA is not able to invoke FSL, but in an inconsistent way.

I ran the whole pipeline for a sample of subjects and everything was OK (with FSL programs running) until all jobs appeared in 'wait' status (mainly when getting to the deterministic tractography step). I terminated all jobs, quitted and loaded the last .PANDA file in order to resume the pipeline. Now all FSL programs failed.

If I go to Matlab and type system('fslroi') I see the correct output. So Matlab is able to talk to FSL.

I am running PANDA with Matlab R2012a on Mac OS 10.9.3. Please find attached the logs folder (I have excluded WM_label and WM_tract_prob folders to reduce file size).

Any help will be greatly appreciated.

Best regards,
Miguel

Hi, Miguel,

Thanks for your interesting in PANDA.

Some subjects were finished (e.g. 00001), but some subjects were failed (e.g. 00038).
The task 'extractB0_00038' of Subject 00038 was failed.

The reason is as following:
fslroi /Volumes/Data/Mike/twins/output_PANDA/00038/tmp/twins_00038_DWI_01.nii.gz /Volumes/Data/Mike/twins/output_PANDA/00038/tmp/data_b0.nii.gz 0 1
ERROR:: Environment variable FSLOUTPUTTYPE is not set!
Please make sure that the appropriate configuration file is sourced by your shell 
e.g. bash or sh users add the line ". ${FSLDIR}/etc/fslconf/fsl.sh"
e.g. tcsh or csh users add the line "source ${FSLDIR}/etc/fslconf/fsl.csh"
extracting b0 volume is done!

Maybe you can check it.
But I'm confused that the task 'extractB0_00001' of subject 00001 was finished.

If you cannot solve the problem according to this instruction, please contact me.

Best regrads

Zaixu

Dear Zaixu,

Thanks for your reply.
I believe my .bash_profile is correct (I think FSL configures it automatically). It looks like this:

# FSL Setup
FSLDIR=/usr/local/fsl
PATH=${FSLDIR}/bin:${PATH}
export FSLDIR PATH
. ${FSLDIR}/etc/fslconf/fsl.sh

# Matlab 2012 configuration
export PATH=${PATH}:/Applications/MATLAB_R2012a.app/bin/

And, as I told you in my first email, typing system('fslroi') in matlab works fine.

Thanks,
Miguel

Hi, Miguel,

Please input 'echo $SHELL' in the terminal, and tell me what is the output.

Best

Zaixu

Dear Zaixu,

The output is /bin/bash

Thanks,
Miguel

Dear Chenxi,

Thanks for your help. After deleting all the outputs and re-running everything again, it finally worked (some jobs got stuck in "wait" status but after quitting and re-loading, it ran correctly).

Best,
Miguel