Good points. I'll keep that in mind. Do you have experience on that?
Cheers,
Cornelius
On Wed, Feb 23, 2011 at 11:41 AM, Andreas Bartsch
<[log in to unmask]> wrote:
> Hi,
>
> a reason I could think of is when the structure-of-interest is not well aligned (e.g. in the brainstem) and thus not well picked up by the ICA/DR (compared to other cortical structures) and to take advantage of the analyses at the single-subject level. In that regards, I think ICA/DR and single-subject seed-based analysis can be complementary / confirmatory under certain circumstances. But yes, the former may usually largely stand on its own.
> Cheers-
> Andreas
>
> ________________________________________
> Von: FSL - FMRIB's Software Library [[log in to unmask]] im Auftrag von Cornelius Werner [[log in to unmask]]
> Gesendet: Mittwoch, 23. Februar 2011 10:46
> An: [log in to unmask]
> Betreff: Re: [FSL] seed based analysis
>
> Hi.
>
> First of all: why would you want to do this? ICA is constructed such
> that the need for the selection of a (potentially biased) seed voxel
> is unnecessary. In terms of "seed" and "target", the ICA equals the
> seed, and the DR output basically equals the target. What is your aim
> doing the same on a seed based method? I am not sure that you aren't
> following circular logic here!
>
> Admittedly, before the advent of DR, one could have chosen (and still
> can choose) an interesting ICA component and define a ROI based on
> that for, e.g., a PPI analysis. Doing a seed based resting state (is
> that so?) analysis would include not only defining your ROI of
> interest, but also ROIs of NO interest, such as CSF and white matter,
> to correct for their (noisy) contributions, which basically means a
> full segmentation of your brains with all what that conveys. Ideally,
> you would also have other biosignals such as heartbeat and respiration
> as regressors of no interest -something you (ideally) do not need in
> Melodic/DR, as those signals get their own components. Seed based
> analyses are tricky!
>
> But to answer at least one of your questions: yes, there are tools for
> signal extraction from a ROI, such as featquery. There have been
> several posts on that. As this is a little laborious, I'd suggest you
> search the archives on that if you are willing to go that way. Search
> for "define ROI from activation" and "featquery" and so forth.
>
> Good luck,
> Cornelius (from not-so-far Aachen)
>
> On Tue, Feb 22, 2011 at 7:50 PM, Perri Carol (di) (PSYCHOLOGY)
> <[log in to unmask]> wrote:
>> Dear FSL group, I have 2 questions for you, I will try to be as clear as possible.
>>
>> I have run melodic and dual regression on a group of patients and controls.
>> I got 25 components, some of them differing spacially on dual regression between the two groups.
>>
>> At this point I would like to study this components better with a seed-based analysis.
>>
>> Here come my questions.
>>
>> 1) Is there an easy way that I can select the voxel / ROI with the highest peak of activation both on the ICA components and on the dual regression output (dr_stage3_ic.._tfce_corrp_tstat..)?
>>
>>
>> 2)how do I do a seed based study? to be more clear how can I select a roi and extract time courses (means of ROI etc.) for post processing ?
>>
>> Thanks in advance for your help!
>>
>> Carol
>
>
>
> --
> Dr. med. Cornelius J. Werner
>
> Department of Neurology
> RWTH Aachen University
> Pauwelsstr. 30
> 52074 Aachen
> Germany
>
> Institute of Neuroscience and Medicine
> MR Physics - INM4
> Research Centre Juelich
> 52425 Juelich
> Germany
>
> ::: Please encrypt confidential data :::
--
Dr. med. Cornelius J. Werner
Department of Neurology
RWTH Aachen University
Pauwelsstr. 30
52074 Aachen
Germany
Institute of Neuroscience and Medicine
MR Physics - INM4
Research Centre Juelich
52425 Juelich
Germany
::: Please encrypt confidential data :::
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