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
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