Hi Martin,
You can get individual time courses or averages using avwmeants
(the output is in text form). This will let you process the values
later
in whatever way you want.
You are correct about the filtered_func_data - it does not have
registration applied to it (but is motion corrected).
I'm not quite sure what is wrong with your Featquery, but your
usage of avwroi is wrong, as you need to use voxel coordinates,
not mm coordinates. All the voxel coordinates should be integers
between 0 and N-1 (inclusive). Using -34 as a coordinate would be
well outside the volume and hence not give you anything except
zeros in the resulting output.
All the best,
Mark
On 15 May 2006, at 19:42, Martin M. Monti wrote:
> FSL masters,
>
> I have 2 ( somewhat unrelated questions)
>
> 1) the filtered_func_data: this is the data with all pre-processing
> steps I asked for, EXCEPT for registration with the High-res and
> MNI-Template? I'm trying a multi-voxel analysis of my data and need
> to pull out time-courses for various regions. Also, is there a way
> to pull out the time-courses associated to EACH voxel within a
> mask? I know avwroi will pull out one average from a given mask. Is
> there any pre-compiled utility to pull out each and all the voxels
> from a mask?
>
> 2) I tried featquery to get a peristimulus plot, but I get more
> event plots than I actually have (i.e. 8 instead of 5!). This is by
> selecting the filtered_func_data and clicking on the PE/%signal
> change and peri-stimulus plot options (I use a mask in MNI
> coordinated and use single-voxel coords). Indeed I think I remember
> someone mentioning that FSL is left to "guess" what an event is. Is
> there a way to instruct FSL as of the timepoints that make an event?
> Alternatively I was wondering whether I could just extract the raw
> timecourse from the filtered_func_data using avwroi and then
> manually create the plots (excel-style). Re this, one thing I'm
> unclear about is, when the syntax requires size: is that number of
> voxels or voxel size? I tried using 1 for all dimensions (e.g.
> avwroi filtered_func_data TC_out -34 1 60 1 4 1) but i then
> couldn't open the image. By changing the 1s to the voxel dimension
> I could successfully create a new image. Is this correct?
>
> cheers
>
> Martin
>
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