Thanks. I've incorporated the sh/bash fix (work around), and this
appears to have corrected the problem. I'll know for sure tomorrow.
Cliff
#################################
Clifford Smith, PhD, ABPP-CN
Board Certified in Clinical Neuropsychology
Assistant Professor of Behavioral Sciences
Rush University Medical Center
O: (312) 942-2893
F: (312) 942-4990
On Jan 7, 2008, at 2:16 PM, Gwenaëlle DOUAUD wrote:
> Mmmm... It may have something to do with 'echo -n'
> which appears to have caused some troubles. (Please
> have a look at the fsl archives searching for "echo
> -n".) If this is indeed the problem, apparently using
> "/bin/echo -n" instead of "echo -n" in the fslvbm_*
> scripts should solve the issue.
>
> Please let me know if it works after changing this.
> Gwenaelle
>
>
> --- Clifford Smith <[log in to unmask]> a écrit :
>
>> Gwenaelle,
>>
>> Thanks for the follow up. Beyond upgrading to
>> Leopard from Tiger, I
>> do not believe I have altered my system. Currently,
>> when running
>> fslvbm_2_template -a I get the series of error files
>> you mention. The
>> *e file are all the same:
>>
>> /bin/sh: line 1: -n: command not found
>>
>> The *.o files are blank.
>>
>> I have not set up the SGE system yet. That is on my
>> To Do list.
>>
>>
>> Cliff
>>
>>
>>
>>
>> #################################
>> Clifford Smith, PhD, ABPP-CN
>> Board Certified in Clinical Neuropsychology
>> Assistant Professor of Behavioral Sciences
>> Rush University Medical Center
>>
>> O: (312) 942-2893
>> F: (312) 942-4990
>>
>>
>>
>> On Jan 7, 2008, at 8:30 AM, Gwenaëlle DOUAUD wrote:
>>
>>> Dear Cliff and Christopher,
>>>
>>> the output you describe here is completely normal.
>> It
>>> just indicates, if you have an SGE system, which
>> job
>>> number is attributed for each task (segmentation,
>>> registration etc.). If you do not have any SGE
>> system,
>>> that should work fine as well but take longer as
>> it
>>> will do all the subjects in series rather than in
>>> parallel.
>>> What I do not understand is why it used to work
>> and it
>>> does not anymore. Have you really run the same
>> kind of
>>> analysis on the *same* computer? Are there any
>> useful
>>> information in any *.o* or *.e* files in FAi?
>>> Especially, if something went wrong (apparently it
>> did
>>> as you have no template_4D_GM), you should have
>> some
>>> error messages in either fslvbm2a.e7378*,
>>> fslvbm2b.e8438e* or fslvbm2c.e11568*.
>>>
>>> In any case, please bear in mind that it can take
>>> *long* to obtain the 4D image if you don't have an
>> SGE
>>> system and a lot of subjects.
>>>
>>> Cheers,
>>> Gwenaelle
>>>
>>>
>>> --- Cliff Smith <[log in to unmask]> a écrit :
>>>
>>>> I'm also running into similar output with
>>>> fslvbm_2_template. I've ran VBM scripts
>>>> successfully in the
>>>> past, and now get a the same output but there is
>> no
>>>> template_4D_GM. Similar difficulties with TBSS.
>>>> Running FSL on two Macs (both with Leopard)
>> produces
>>>> similar output.
>>>>
>>>> Running segmentation: ID=7378
>>>> Running registration: ID=8438
>>>> Creating template: ID=11568
>>>> Study-specific template will be created, when
>>>> complete, check FAi/template_4D_GM as a movie
>> loop
>>>> in fslview
>>>>
>>>
>>>
>>>
>>>
>>>
>>
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>
>
>
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