Problem solved. The script was copied from my email program and then dashes became som kind of long dashes in the text editor. I noted when I rewrote using the keyboard.
Strange that bet2 didn't mind the long dashes.
Thanks for your help, much appreciated.
best nick
Niklas Lenfeldt, MD, Civing, Mj
Umeå universitet
070-60966876
________________________________________
Från: FSL - FMRIB's Software Library [[log in to unmask]] för Mark Jenkinson [[log in to unmask]]
Skickat: den 21 mars 2011 22:30
Till: [log in to unmask]
Ämne: Re: [FSL] SV: [FSL] SV: [FSL] SV: [FSL] bet v bet2?
Of course you can reply tomorrow!
I can't guarantee that we will be answering at 7am UK time though. :)
All the best,
Mark
On 21 Mar 2011, at 21:14, Niklas Lenfeldt wrote:
> I am afraid I am at home now, and the linux machine is at work. I will test your advice tomorrow. You are very kind, is it OK that I come back tomorrow, around 0800 CET?
>
> Best nick
>
>
>
> Niklas Lenfeldt, PhD, MSc E.P., Maj SWE A
> Clinical neuroscience, Umeå university
> Email: [log in to unmask]
> Phone: +46706096687, +46733294165
>
>
> -----Ursprungligt meddelande-----
> Från: FSL - FMRIB's Software Library [mailto:[log in to unmask]] För Mark Jenkinson
> Skickat: den 21 mars 2011 22:10
> Till: [log in to unmask]
> Ämne: Re: [FSL] SV: [FSL] SV: [FSL] bet v bet2?
>
> Hi,
>
> It looks like your environment is being disturbed in some way.
> If you try the following from the command line (typing it yourself):
> bet data preprocessData_brain -m -f 0.15
> in one of your directories, then does this work or give you an error too?
> I suspect that typing it from the command line will work and that
> something in your script is causing the problem with environment variables.
>
> The reason I say this is that bet is a script and calls bet2 internally, but
> if it cannot find bet2 because FSLDIR is broken (or something like that)
> then this would cause an error like you see.
>
> Is there anything more to the script?
> And how are you running the script?
> Is it running on your local machine or on a cluster?
>
> All the best,
> Mark
>
>
>
> On 21 Mar 2011, at 21:04, Niklas Lenfeldt wrote:
>
>> List=(arrays pointing to subject's folder)
>>
>> For fn in ${list[@]}
>> do
>> cd $fn
>> bet data preprocessData_brain -m -f 0.15
>> dtifit -k data -o dti -m preprocessData_brain_mask -r *.bvec -b *.bval
>> done
>>
>> I have similar problems with dtifit. data is the output file from eddy_correct. Bvec and bval files lie in each of the list folders. I'm not completely used to linux programming yet so any help is much appreciated. If bet is replaced with bet2, then it works.
>>
>> nick
>>
>>
>> Niklas Lenfeldt, PhD, MSc E.P., Maj SWE A
>> Clinical neuroscience, Umeå university
>> Email: [log in to unmask]
>> Phone: +46706096687, +46733294165
>>
>>
>> -----Ursprungligt meddelande-----
>> Från: FSL - FMRIB's Software Library [mailto:[log in to unmask]] För Mark Jenkinson
>> Skickat: den 21 mars 2011 21:56
>> Till: [log in to unmask]
>> Ämne: Re: [FSL] SV: [FSL] bet v bet2?
>>
>> Dear Nick,
>>
>> Can you send me the command you are trying to run?
>> It sounds like bet exists and is working on your system.
>> It is likely to be an error in your command line, as that is
>> the typical response to such an error.
>>
>> All the best,
>> Mark
>>
>>
>> On 21 Mar 2011, at 20:50, Niklas Lenfeldt wrote:
>>
>>> Linux 6.5 redhat. The machine returns the "help" document for bet (as if I had written bet -h)
>>>
>>> best
>>>
>>> nick
>>>
>>>
>>> -----Ursprungligt meddelande-----
>>> Från: FSL - FMRIB's Software Library [mailto:[log in to unmask]] För Mark Jenkinson
>>> Skickat: den 21 mars 2011 20:14
>>> Till: [log in to unmask]
>>> Ämne: Re: [FSL] bet v bet2?
>>>
>>> Dear Nick,
>>>
>>> You should be able to call bet - it should work in all versions.
>>> What platform are you on and what error do you get when you
>>> try and run bet?
>>>
>>> All the best,
>>> Mark
>>>
>>>
>>> On 21 Mar 2011, at 18:30, Niklas Lenfeldt wrote:
>>>
>>>> Hi all,
>>>>
>>>> I have a question on bet v bet2. My version of fsl does not respond when calling bet, but it responds properly to bet2. Is it so that in the latest versions you cannot call bet anymore, you have to call bet2 directly? There was some lines implying this in the help section.
>>>>
>>>> Any info on this would be most valuble.
>>>>
>>>> Best nick
>>>
>>
>
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