Print

Print


Hi, 

Thank you for your repsonse and advise. 
I spoke with our systems manager about your questions of OS, hardware and 
FSL version. We also tried again together to locate and fix the error. We ran 
into the following problems: 
 

The program feat starts a lot of featX_YY programs. One of them is 
feat3b_flame using -t ./.flame as a command file option. However at the time 
of submitting the .flame file only contains dummy as a program to execute. So 
the jobs submitted to the cluster all fail. Afterwards the .flame files contains 
flameo commands. We have no idea where the latter come from. We found line 
in feat where dummy is added to the .flame file but we don't understand why 
this is done.



We think  this is the reason why the error /apps/fsl/current/bin/flameo --
cope=filtered_func_data --
> vc=var_filtered_func_data --dvc=tdof_filtered_func_data --mask=mask -- 
> ld=stats --dm=design.mat --cs=design.grp --tc=design.con  --runmode=fe 
occurs in the GUI.
Indeed when we run one of these flameo commands directly from the 
command line it works. We tested our hypothesis by changing the fsl_sub 
script to execute all jobs without submitting to the grid and indeed this too 
worked fine. For some reason no dummy commands were written to the .flame 
file at that time...


Do you have a solution for this problem?

 

OS: Clustervision OS 5.0 (based on Redhat Enterprise 5 and CentOS 5)

Arch: 64bit

FSL: 4.1.2

kernel: 2.6.18

Many thanks

Judith & Bart (systems manager)



-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of 
Steve Smith
Sent: woensdag 5 augustus 2009 8:02
To: [log in to unmask]
Subject: Re: [FSL] high level analysis FEAT

Hi,

This is a very strange looking error - I suspect either that there is  
something wrong with your computer or file system mounting, or it is a  
weird operating system that we've not seen before. Exactly what  
hardware and OS are you running, and which version of FSL?  Have you  
tried rebooting your computer?

Cheers.


On 4 Aug 2009, at 08:10, judith wrote:

> Hi,
>
> I am having troubles performing a high level analysis using low  
> level feat
> directories.
> For low level processing I was not experiencing any trouble.  
> However, using
> these low level feat directories in a high level analysis, for  
> example a simple
> average of one group using mixed effects or fixed effects, the high  
> level stats
> crashes at the following command:
> /apps/fsl/current/bin/flameo --cope=filtered_func_data --
> vc=var_filtered_func_data --dvc=tdof_filtered_func_data --mask=mask --
> ld=stats --dm=design.mat --cs=design.grp --tc=design.con  --runmode=fe
> Warning: no access to tty (Bad file descriptor).
> Using this command by entering it in the terminal, it runs without  
> any problems
> the stats, so the data needed are available.
> However since poststats cannot be ran seperatly, I cannot perform the
> analysis needed.
> Does anyone have an idea wat I am doing wrong?
>
> I will add the whole command line below:
> Higher-level stats
>
> cat ../design.lcon | awk '{ print  }' > design.lcon
> /apps/fsl/current/bin/flameo --cope=filtered_func_data --
> vc=var_filtered_func_data --dvc=tdof_filtered_func_data --mask=mask --
> ld=stats --dm=design.mat --cs=design.grp --tc=design.con  --runmode=fe
> Warning: no access to tty (Bad file descriptor).
> Thus no job control in this shell.
> dummy: Command not found.
> Warning: no access to tty (Bad file descriptor).
> Thus no job control in this shell.
>
> /bin/rm -f stats/zem* stats/zols* stats/mask* ; /bin/mv dof stats
> Warning: no access to tty (Bad file descriptor).
> Thus no job control in this shell.
>
> Post-stats
>
> couldn't change working directory
> to "/mic/jvhoev2/data_taal/data/CO/FE_single_group_average.gfeat/ 
> cope1.feat
> /stats": no such file or directory
>    while executing
> "cd ${FD}/stats"
>    (procedure "feat5:proc_poststats" line 50)
>


---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director,  Oxford University FMRIB Centre

FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
+44 (0) 1865 222726  (fax 222717)
[log in to unmask]    http://www.fmrib.ox.ac.uk/~steve
---------------------------------------------------------------------------