hi, Christian,
I still have a question of doing post-stats in MELODIC. I have tried
your suggestions of how to do mixture modelling after ICA estimation is
done. So by using the following call:
melodic -i <bgimage> --ICs=melodic_IC --mix=melodic_mix [
--smode=melodic_Smode ] [--Tdes=design.mat --Tcon=design.con ] -v
--report [ --Ostats ]
I will get the thresholded spatial maps of the ICs (posterior
probability p<0.5), and after clicking the maps, the raw Z-maps and
probability maps will appear.
I am wondering how melodic does the Z-transformation based on the input
"melodic_IC" and "melodic_mix", because it needs the standard deviation
of the background noise to do the transformation, right? Or the
information of the residual noise is alreay included in the input? Since
this call doesn't do PICA estimation from the start, I am not sure about
the noise estimation part. I guess I am missing some point here ...
Thank you very much for any advice!
Best Regards,
Yanmei
Christian F. Beckmann wrote:
> Hi
>
> yes, you can call the mixture model fitting and report generation
> using the command line version of melodic
>
> melodic -i <bgimage> --ICs=melodic_IC --mix=melodic_mix [
> --smode=melodic_Smode ] [--Tdes=design.mat --Tcon=design.con ] -v
> --report [ --Ostats ]
>
> <bgimage> needs to be in the space of the IC maps in melodic_IC and
> the optional smode adds subject-modes to the report. The --Tdes and
> --Tcon options tell melodic which GLM design to use for post-hoc OLS
> fitting - you can do the same for GLM fitting to the smdes, simply add
> the --Sdes= and --Scon= options . Finally, the --Ostats option makes
> sure that the mixture model probability maps get saved.
> hope this helps
> Christian
>
>
> _______________________________________________
> Christian F. Beckmann, DPhil
> Senior Lecturer, Clinical Neuroscience Department
> Division of Neuroscience and Mental Health
> Imperial College London
> Hammersmith Campus, Rm 247, Cyclotron Bldg
> Du Cane Road, London W12 0NN, UK
> Tel.: +44 (0) 208 383 8598 --- Fax: +44 (0) 208 383 2029
>
> Email: [log in to unmask] <mailto:[log in to unmask]>
> http://www.imperial.ac.uk/medicine/people/c.beckmann/
>
>
>
> On 18 Sep 2007, at 18:52, Yanmei Tie, Ph.D. wrote:
>
>> Hi Steve,
>>
>> Sorry for the confustion. I mean, is there a way of ONLY performing
>> the post-stats? Like, I have IC z-maps already, and just want to do
>> mixture modeling, and/or post-hoc GLM analyses of IC time courses
>> against a GLM design matrix ...
>>
>> Thank you very much!
>> yanmei
>>
>> Steve Smith wrote:
>>
>>> Hi - I'm a little confused as this is exactly the default behaviour
>>> that you get when you run MELODIC from the GUI.
>>> Cheers.
>>>
>>>
>>> On 18 Sep 2007, at 14:49, Yanmei Tie wrote:
>>>
>>>> hi all,
>>>>
>>>> I wonder if there is a way that I can perform post-stats (Gaussian/
>>>> Gamma
>>>> mixture modeling and alternative hypothesis test with
>>>> thresholding) using IC
>>>> z-maps as input. Is there an option in melodic command-line?
>>>>
>>>> Thanks very much for any suggestions.
>>>>
>>>> Best regards,
>>>> yanmei
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------
>>> ---
>>> 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] <mailto:[log in to unmask]>
>>> http://www.fmrib.ox.ac.uk/~steve
>>> ------------------------------------------------------------------------
>>> ---
>>
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