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FSL  August 2007

FSL August 2007

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Subject:

Re: multi-session / subject MELODIC

From:

Vitaly Napadow <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Thu, 16 Aug 2007 10:32:57 -0400

Content-Type:

TEXT/PLAIN

Parts/Attachments:

Parts/Attachments

TEXT/PLAIN (89 lines)

thank you, Christian. I think I understand - for my purposes, to test for 
spatial (not tempopral) differences, I will continue with my past 
approach...

regards,

vitaly


On Thu, 16 Aug 2007, Christian Beckmann wrote:

> Hi
>
> On 15 Aug 2007, at 17:20, Vitaly Napadow wrote:
>
>> hi all
>> 
>> firstly, thanks for finally pushing this out. i think we were all chomping
>> at the bit looking forward to the new release and it feels great to finally
>> play with the new tools.
>> 
>> i had completed an analysis of resting state data but want to go back and
>> try the new tools now. i have 15 subjects and two separate rest runs that i
>> am comparing from each subject. i assume i want to use Multi-session
>> temporal concatenation to contrast the two rest runs.
>
> Yes, temporal concatenation is probably what you want, though you still will 
> need to decide on what exactly you want to compare between runs, e.g. the 
> amount of variance in the associated time course (as a measure of volatility) 
> or any other quantity you could come up with such as mean level
>
>> so as not to compare
>> apples to oranges, i want to contrast specific resting state networks. my
>> question is, if i specify and 2nd level design.mat and design.con file with
>> a 1 -1 contrast how will i know which resting state networks (evident on
>> group maps) are associated with or correspond to which 2nd level output
>> components?
>
> Don't quite understand the question. In the new release version you have the 
> option of testing (in the GLM sense) each associated time course and each 
> associated session/subject mode using design and contrast matrices. The GLm 
> fit will be performed separately for each time course and/or subject session 
> mode vector.
>
>> 
>> alternatievly, if i already did single-subject analyses and have mixing
>> matrices etc with components corresponding to known resting networks and
>> which can be pulled out to input into a 2nd level group analysis, are my
>> options to contrast on a 2nd level the same as before?
>
> fundamentally yes, the main difference being that in the case of separate 
> analyses you're bound to have differences in e.g. the default-mode network 
> between subjects. In the case of temporal concatenation or full TICA you 
> effectively fix the spatial maps to be identical and only allow the time 
> courses to be different.
> hope this helps
> Christian
>
>> thanks
>> 
>> vitaly
>> 
>
> ____
> Christian F. Beckmann
> University Research Lecturer
> Oxford University Centre for Functional MRI of the Brain (FMRIB)
> John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK.
> [log in to unmask]	http://www.fmrib.ox.ac.uk/~beckmann
> tel: +44 1865 222551			fax: +44 1865 222717
>
>
>

-- 
|`~~~~~~~~~~~~~~~~~\|/~~~~~~~~~~~~~~~~~'|

Vitaly Napadow, Ph.D., Lic.Ac.
Assistant Professor
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
CNY 149-2301, 13th St.
Charlestown, MA 02129
phone: (617) 724-3402
fax:   (617) 726-7422
www.nmr.mgh.harvard.edu/~vitaly

|`~~~~~~~~~~~~~~~~~/|\~~~~~~~~~~~~~~~~~'|

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