Hi
I agree with Wolf here - it makes perfect sense to run as much as
possible from the command line in cases like this. Easiest option is
to check the log files from a completed GUI-based analysis to get a
list (and the order of) command line calls to the various FSL tools.
You can then replace/add options as you see fit (and also sanity-check
the analysis along the way ;)
hth
Christian
On 13 May 2009, at 16:34, wolf zinke wrote:
> Hi,
>
> I would recommend to do all the preprocessing (motion correction, bet)
> prior running Melodic, since the defaults are set to work optimally
> with
> human brains, but this is suboptimal for other animals. As far as I am
> aware of, Melodic does not use the correction parameter anyway, so you
> would not loose anything, but you might ensure optimal motion
> correction.
>
> hope this helps,
> wolf
>
>
> Roman Loonis wrote:
>> I am analyzing resting network activity in the macaque monkey by
>> applying fsl's MELODIC
>> ICA to functional data. The MELODIC registration, which uses flirt,
>> fails to appropriately
>> register the images. I can only properly align the two images in
>> FLIRT when I use the cost
>> function "normalised correlation." Unfortunately, I do not have
>> access to this option in
>> MELODIC ICA_gui. Is there any easy way I can include this cost
>> function into MELODIC ICA's
>> registration?
>>
_______________________________________________
Christian F. Beckmann, DPhil
Senior Lecturer, Clinical Neuroscience Department
Division of Neuroscience and Mental Health
Imperial College London, Hammersmith Campus
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http://www.imperial.ac.uk/medicine/people/c.beckmann/
Senior Research Fellow, FMRIB Centre
University of Oxford
JR Hospital - Oxford OX3 9DU
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http://www.fmrib.ox.ac.uk/~beckmann
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