Gwenaelle
I am new here. Hope you can help. I am having the same problem as discussed
below.
I am running on MacOsX10.6.2 i5
trying to do fsl-vbm but the
fslvbm_2_template -N, after running for several hours, asked me to check
the template_4D image. This was not present in addition all my fslvbm.e and
o files are empty (zero bytes)
if i have to change the echo -n how sjhould I do - I dont want to make any
fatal errors on the scripts!!
Thanks in advance
Lena
On Mon, 7 Jan 2008 21:16:40 +0100, Gwenaëlle DOUAUD
<[log in to unmask]> 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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