Hi.
On Mon, 23 Aug 2004, Haiying Liu wrote:
> 1. Inside a FEAT Report (report.html), say I have the following
> thresholded activation images: zstat1-C1 ((1)), zstat2-C2 ((1)),
> zfstat1-F1 (C1 & C2), zfstat2-F2 (C1), and zfstat3-F3 (C2)
>
> then I have 5 time series plots. I noticed that I can find the sinusoid
> curve parameters (full model fit) for both zstat1-C1 and zstat2-C2 from
> design.fsf; they correspond to basic waveform shape for EV1 and EV2. Where
> can I find the sinusoid curve parameters (definitions) for all F tests?
> I want to redraw time series plots in another tool for any voxel a user
> specifies.
Just the same as with the T contrasts; if you click on the time series
with the title "zfstat1...." you'll get more plots realted to the f-test,
etc.
> 2. I assume all thresh_*** volumes (thresh_zfstat1.hdr/img,
> thresh_zfstat2.hdr/img, thresh_zfstat3.hdr/img, thresh_zstat1.hdr/img,
> thresh_zstat2.hdr/img, ...) are already in the same space as
> filtered_func_data.hdr/img. When I overlay any of the thresh_*** volumes
> onto filtered_func_data.hdr/img, I don't need to do any transform. Am I
> right?
That's right.
> 3. If I want to overlay thresh_zstat1.hdr/img onto the standard brain and
> my own structural scan, I guess I will do the following:
>
> a. Use flirt to co-register thresh_zstat1.hdr/img and the standard
> brain; then I get a new volume of thresh_zstat1.hdr/img. Then overlay the
> new volume onto the standard brain.
>
> b. Use flirt to co-register thresh_zstat1.hdr/img and my own structural
> scan; then I get a new volume of thresh_zstat1.hdr/img. Then overlay the
> new volume onto the structural scan.
Well, there's easier ways. Assuming that you setup and ran registration
within the main FEAT GUI then all the transforms you need are already
inside the reg subdirectory inside the FEAT output directory. You can
either apply these using FLIRT to the thresh_ images, or, even more
easily, use the Renderhighres GUI to do this for you.
Cheers, Steve.
Stephen M. Smith DPhil
Associate Director, FMRIB and Analysis Research Coordinator
Oxford University Centre for Functional MRI of the Brain
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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