Well - at least on my laptop it doesn't run in the background if you
start it on the command line - are you sure you don't have SGE_ROOT
setup? Do you have the latest FSL version?
Cheers.
On 26 May 2009, at 13:07, Alex Fornito wrote:
> Not as far as I'm aware. The reason I say all the subjects run
> simultaneously is that featwatcher pops up for each of the subjects
> in SUBS
> shortly after excuting the script. Is that normal?
>
>
> On 26/05/2009 13:04, "Steve Smith" <[log in to unmask]> wrote:
>
>> Hi - the latest version should run in the foreground - unless you are
>> using a cluster setup like SGE?
>> Cheers.
>>
>> On 26 May 2009, at 12:52, Alex Fornito wrote:
>>
>>> I see. Thanks.
>>>
>>> This may seem a stupid question, but I have now generated separate
>>> design.fsf files for each subject and tried to run feat on each .fsf
>>> using a simple loop; e.g.,
>>>
>>> SUBS=`cat SubjectList.txt`
>>> for S in $SUBS
>>> do
>>> feat ${S}_design.fsf;
>>> done
>>>
>>> However, the feat binary seems to set ALL the analyses running in
>>> the background, instead of running them in sequential order. That
>>> is, if SUBS contains 10 subjects, all 10 subjects’ are set running
>>> near-simultaneously, which really slows the system down.
>>>
>>> Is there anyway to get feat to run sequentially, one subject at a
>>> time, using a loop for the command line?
>>>
>>> Thanks again,
>>> Alex
>>>
>>>
>>>
>>> On 25/05/2009 16:55, "Eugene Duff" <[log in to unmask]> wrote:
>>>
>>>> Hi Alex
>>>>
>>>> 2009/5/25 Alex Fornito <[log in to unmask]>
>>>>> Hi all,
>>>>> I am trying to perform a seed-based corrrelation analysis of
>>>>> resting-state
>>>>> fMRI data. I have been trying to set-up the first level analysis
>>>>> in a pilot
>>>>> sample using the gui. I'm assuming that the timecourse of my seed
>>>>> region
>>>>> should be entered as the EV, with convolution turned off.
>>>>> However, the gui only allows me to enter 1 text file even though I
>>>>> have 10
>>>>> subjects' data loaded in. As I have one unique regressor per
>>>>> subject (i.e.,
>>>>> each individual's seed timecourse), I need to enter one text file
>>>>> per
>>>>> subject. Is there any way to do this through the gui, or should I
>>>>> just run
>>>>> the analysis for one person and use the resulting script?
>>>> Yes, you'll need to run them separately (using the same template
>>>> design file adjusted for each ).
>>>>
>>>>>
>>>>>
>>>>> In addition, do you have any recommendations re: how the regressor
>>>>> values
>>>>> should be scaled, given that I also have a number of confound EV's
>>>>> in the
>>>>> model (e.g., motion parameters, white matter, csf, global signal
>>>>> timeseries,
>>>>> etc.)?
>>>>>
>>>> The scaling of your regressors has no influence on the modelling.
>>>> It is only important that EVs that are being contrasted against
>>>> each other are scaled consistently.
>>>> Cheers,
>>>> Eugene
>>>>> Thanks for your help,
>>>>> Alex
>>>>
>>>>
>>>
>>> --
>>>
>>> Alex Fornito
>>> CJ Martin Post-Doctoral Fellow
>>> Brain Mapping Unit
>>> Department of Psychiatry
>>> University of Cambridge
>>> Downing Site
>>> Downing St, Cambridge
>>> UK CB2 3EB
>>>
>>> Email: [log in to unmask]
>>> Phone: +44 (0) 1223 764670
>>> Fax: +44 (0) 1223 336581
>>>
>>> Australian Details:
>>>
>>> Melbourne Neuropsychiatry Centre
>>> National Neuroscience Facility
>>> Levels 1 & 2, Alan Gilbert Building
>>> 161 Barry St
>>> Carlton South 3053
>>> Victoria, Australia
>>>
>>> Email: [log in to unmask]
>>> Phone: +61 3 8344 1861
>>> Fax: +61 3 9348 0469
>>>
>>
>>
>> ---------------------------------------------------------------------------
>> 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
>> ---------------------------------------------------------------------------
>
> --
>
> Alex Fornito
> CJ Martin Post-Doctoral Fellow
> Brain Mapping Unit
> Department of Psychiatry
> University of Cambridge
> Downing Site
> Downing St, Cambridge
> UK CB2 3EB
>
> Email: [log in to unmask]
> Phone: +44 (0) 1223 764670
> Fax: +44 (0) 1223 336581
>
> Australian Details:
>
> Melbourne Neuropsychiatry Centre
> National Neuroscience Facility
> Levels 1 & 2, Alan Gilbert Building
> 161 Barry St
> Carlton South 3053
> Victoria, Australia
>
> Email: [log in to unmask]
> Phone: +61 3 8344 1861
> Fax: +61 3 9348 0469
>
---------------------------------------------------------------------------
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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