Hi Jesper,

Thanks for your response. I had done what you've suggested, except I did 
not use the verbose option :)
Anyway, it seems my problem as probably nothing to do with the FSL 
scripts or my data: when I tried it last Friday, the fnirt command ran 
for more than 3 hours without outputting anything before I killed it. 
The analysis of the same data set however ran fine on 2 other machines...
And today... it works on the machine that used to fail! Another fun 
mystery to solve for our system administrator...

Thanks for your help,

Stephane


Jesper Andersson wrote:
> Hi Stephane,
>
> I am afraid I cannot really say what might have gone wrong from this 
> info. Could you please go into one of the directories where it failed 
> and then cut and paste the fnirt command from the pertinent log-file 
> into a terminal window and then add --verbose at the end of the 
> command, i.e.
>
> /usr/local/fsl4.1.0/bin/fnirt --in=highres_head 
> --aff=highres2standard.mat --cout=highres2standard_warp 
> --iout=highres2standard --jout=highres2standard_jac 
> --config=T1_2_MNI152_2mm --ref=standard_head --refmask=standard_mask 
> --warpres=10,10,10 --verbose
>
> If it fails again (I hope it does) could you then send me all the 
> output that was written to the screen?
>
> Jesper
>
>
> On 12 Sep 2008, at 18:01, Stephane Jacobs wrote:
>
>> Hello FSL!
>>
>> I'm trying to run the latest version of FSL, including FNIRT, and 
>> have some
>> strange problems with it: on some data sets it runs just fine, but with
>> others, it doesn't complete but doesn't throw any error message. The 
>> error
>> comes up only when slicer tries to use the output that FNIRT never 
>> created.
>>
>> When I look at the log, it varies: either I only have the FNIRT command
>> without the usual "Setting subsampling, Setting reg mode, Setting 
>> lambda",
>> or just a few iterations of those, or it can even look OK, but the 
>> output is
>> consistently missing in all cases!
>>
>> I have attached 3 different logs illustrating this. Any help would as 
>> always
>> be greatly appreciated.
>>
>> Thanks,
>>
>> Stephane
>>
>> --:::::::::::::::::::::::::::::::::::::::::::::::::::
>> Stephane Jacobs
>>
>> Postdoctoral Research Associate
>> Human Neuroimaging and Transcranial Stimulation Lab
>> Department of Psychology
>> 1227 University of Oregon
>> Eugene, OR 97403 - USA
>>
>> Email: [log in to unmask]
>> Tel: (1) 541-346-4184
>> :::::::::::::::::::::::::::::::::::::::::::::::::::
>>
>> <report_logs.zip>
>
>

-- 
:::::::::::::::::::::::::::::::::::::::::::::::::::
Stephane Jacobs

Postdoctoral Research Associate
Human Neuroimaging and Transcranial Stimulation Lab
Department of Psychology
1227 University of Oregon
Eugene, OR 97403 - USA

Email: [log in to unmask]
Tel: (1) 541-346-4184
:::::::::::::::::::::::::::::::::::::::::::::::::::