Excellent, thanks a lot!
Have a nice weekend,
Cornelius
On Fri, Apr 8, 2011 at 10:37 AM, Stephen Smith <[log in to unmask]> wrote:
> Hi
>
> On 7 Apr 2011, at 11:09, Cornelius Werner wrote:
>
> I am trying to complement a traditional GLM analysis of a rather
>
> lengthy and complex fMRI study with MELODIC results. I am prticularly
>
> interested in components correlating with event timecourses (six
>
> types), which were displayed randomly across subjects. This means that
>
> tensorial ICA is out. I ran individual ICA on all single subjects and
>
> am now identifying correlated maps manually in order to somehow
>
> group-average them later. This is where I need help:
>
> - can I get component numbers correlating with my EVs in an automated
>
> fashion for each subject?
>
> Yes- in the GUI, final tab, you can enter a design matrix for exactly this
>
> purpose - the results from correlating the component timecourses against the
>
> model you provide are included in the web-page reporting
>
> That's what I did. Can I filter out significant ones via an existing
> script? I suppose that there is some perl or python way of parsing the
> html-file, but I am not that good at this. Well, I still can do it
> manually.
>
> Probably the easiest way to script this is to just regress your model
> against the melodic_mix timecourses, e.g. in matlab/python?
> Note that if you start with a group-ICA, you will want to use the first
> stage of dual-regression to get subject-specific timecourses for each group
> component - and then regress those timecourses against your model.
>
> - which data should I feed into a group analysis?
>
> I guess you need to identify (ideally just one strongest) component from the
>
> above to feed into the group-level result…..
>
> Or - you could use concat-mode group-ICA and dual-regression, to maybe get
>
> the above without utilisation of the GLM
>
> In this case, I would need to check the dr_stage1 output files for a
> correlation with my EVs of interest, wouldn't I?
>
> Oh - yes - that's right - the point I just made above.
>
> Do I need to convolve
> my EV with an HRF, as the timecourses in dr_stage1 are sampled from
> the data?! Or is the dr_stage1 output already "deconvolved"?
>
> no it's not deconvolved - it matches the data - so if your model has not
> already been HRF convolved then yes you should do that - e.g. easy with
> FEAT.
> design.mat HAS been convolved in FEAT.
>
> Actually,
> I am not sure about DR in this case - there are no separate groups,
> all subject got to see all stimuli, but in a randomised fashion.
>
> That's fine - DR is fine for one group also.
> Cheers
>
> Sorry
> if I didn't make that clear. In any case, thanks a lot for the help,
> as always!
>
>
>
>
>
> Cheers,
> Cornelius
>
>
> For the latter part, I imagined fslmerge-ing maps that a) belong to
>
> one EV-type and b) show spatial similarity as determined by fslcc,
>
> meaning separate parietal and frontal maps relating to a particular
>
> would not be thrown together (but analysed separately). Then I'd be
>
> runnning randomise on the image stack. But: which data should enter
>
> this set: the raw component from melodic_IC or the probmap?
>
> Sure - or you can do what i suggest above. You could try either using
>
> melodic_oIC (which doesn't include normalisation using the 'noise') or the
>
> z-stat version melodic_IC, depending on your preference
>
> Cheers
>
> And how
>
> should I deal with subjects not exhibiting a fitting map? Did anyone
>
> perform something similar before?
>
> Thanks for any help,
>
> Cornelius
>
> --
>
> Dr. med. Cornelius J. Werner
>
> Department of Neurology
>
> RWTH Aachen University
>
> Pauwelsstr. 30
>
> 52074 Aachen
>
> Germany
>
>
>
> ---------------------------------------------------------------------------
>
> 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
>
> ---------------------------------------------------------------------------
>
>
>
>
>
>
>
> --
> Dr. med. Cornelius J. Werner
> Department of Neurology
> RWTH Aachen University
> Pauwelsstr. 30
> 52074 Aachen
> Germany
>
>
>
> ---------------------------------------------------------------------------
> 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
> ---------------------------------------------------------------------------
>
>
>
>
--
Dr. med. Cornelius J. Werner
Department of Neurology
RWTH Aachen University
Pauwelsstr. 30
52074 Aachen
Germany
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