Hi - yes, we are planning on making simple SGE setup instructions
available once we have a chance, sorry we haven't done that yet.
Various binaries, including linux, are available at
http://gridengine.sunsource.net/downloads/60/download.html
Hopefully the setup is easy - we'll try to finish our setup
instructions/scripts ASAP.
Cheers, Steve.
On 21 Aug 2007, at 17:47, Roderick McColl wrote:
> For those of us who are unfamiliar with SGE and who liked to use
> the 3.3 approach to parallelizing tbss_2_reg,
> do you have any instructions for where to get SGE, and what a
> suitable config might be to parallelize the 4.0 code?
> I don't see from Sun's web site a SGE for Linux.
>
> Thanks
>
> -roddy
>
>>>> Steve Smith <[log in to unmask]> 8/20/2007 4:34 AM >>>
> Hi,
>
> You can't run tbss_2_reg from a second shell in parallel I'm afraid -
> that's the cause of the problem here. This mechanism for speeding
> things up was in the old version - to speed things up in the new
> version through parallelisation relies on having SGE, which handles
> the parallelisation much more properly than the old method.
>
> Cheers, Steve.
>
>
> On 20 Aug 2007, at 09:56, Lars Tjelta Westlye wrote:
>
>> Hi again,
>> I reorinted my data and tried running the script again from the
>> main TBSS
>> folder (../FAi), but the error message persists. I have uploaded my
>> test
>> data (2 subjects) with the following ref nr: 159404. The same error
>> message occurs when I try to run the script from a second shell to
>> speed
>> things up, that is before the the first shell gives me an error. Any
>> thoughts on what might be going wrong? It seems to me that
>> the .command
>> file is not generated.
>>
>> Thank you for your help.
>>
>> Best,
>> Lars
>>
>>
>>> Hi - it sounds possibly like you're not running the TBSS scripts
>>> from
>>> the right directory - make sure all the files are present in the FAi
>>> directory and that you are one level up from that before running
>>> tbss_2_reg (you should remove all FAi/*.msf files before rerunning).
>>>
>>> If it still doesn't work then please tar up the whole TBSS working
>>> directory and upload it to us to check.
>>>
>>> I would indeed recommend using fslswapdim to reorient your data
>>> before running TBSS as the affine registration in IRTK is not quite
>>> as robust to initial orientation as FLIRT.
>>>
>>> Cheers, Steve.
>>>
>>>
>>> On 17 Aug 2007, at 17:32, Lars Tjelta Westlye wrote:
>>>
>>>> Hi,
>>>>
>>>> running tbss_2_reg -T on 10 test subjects gives me the following
>>>> error
>>>> message (after a couple of hours):
>>>>
>>>> sed: can't read .commands: No such file or catalog
>>>> sed: can't read .commands: No such file or catalog
>>>> sed: can't read .commands: No such file or catalog
>>>> sed: can't read .commands: No such file or catalog
>>>> sed: can't read .commands: No such file or catalog
>>>> sed: can't read .commands: No such file or catalog
>>>> sed: can't read .commands: No such file or catalog
>>>> sed: can't read .commands: No such file or catalog
>>>> sed: can't read .commands: No such file or catalog
>>>> 11283
>>>>
>>>> Any clues? The .command file is in the TBSS folder.
>>>>
>>>> My data seem to have a different orientation than that of the
>>>> target
>>>> (FMRIB52_1mm), i.e. in sagittal view in Fslview anterior is to the
>>>> left on
>>>> the monitor. Even though the letters denoting the directions are
>>>> correct,
>>>> could this be causing any problems registering to the FMRIB target?
>>>> All
>>>> volumes are in radiological orientation, according to fslorient.
>>>>
>>>> Could what is causing this problem also be the reason why I can't
>>>> run the
>>>> script from different shells from the beginning?
>>>>
>>>> Thanks again!
>>>>
>>>> Lars
>
>
> ----------------------------------------------------------------------
> --
> ---
> 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
> ----------------------------------------------------------------------
> --
> ---
------------------------------------------------------------------------
---
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
------------------------------------------------------------------------
---
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