Hello David,
> I'm trying to extract the mean timecourse (or the voxel timecourse
> respectively) of an ROI of the Anatomy Toolbox from a dataset for every
> volume of the dataset. In this case, I'm using the MoAE Dataset from
> your website. What I essentially want is a mean value for every volume
> of the data for some ROIs which I chose from the Anatomy Toolbox or any
> other ROI for that matter. Up to now I only managed to extract the
> timecourses of significant clusters after calculating the GLM. What I
> essentially want is the timecourses of ROIs/clusters no matter if they
> are significant or not.
what you want is easily accomplished using spm functionality, using
functions such as spm_select, spm_vol, and spm_read_vols, in that order.
This will, if you select all images in a time series, give you a 4D
matrix where time is the fourth dimension (note that this will only
proceed without errors if the images you select are in voxelwise
alignment, i.e., untouched, resliced, or normalized). You can then get
the timecourse from any voxel you are interested in (say, the one at
voxel location 30/30/30) by selecting it from the matrix:
vols = spm_read_vols(spm_vol(spm_select(Inf, 'image', 'Select time
series images')));
vx = [30 30 30];
tc = squeeze(vols(vx(1), vx(2), vx(3), :));
figure; plot(tc);
You can then generalize that to search over a specific region you are
interested in. For easy determination of voxel coordinates, I recommend
findn from the Mathworks file exchange. One thing to keep in mind,
though, is that this will be a little bit less easy if your ROI has
different dimensions than your fMRI data.
> I hope you can help me out :)
I hope so, too :)
Cheers,
Marko
PS: Beware of the fact that what spm provides via the interface is not
necessarily the mean, but may be the first eigenvariate. See the list
archives for some more details.
--
____________________________________________________
PD Dr. med. Marko Wilke
Facharzt für Kinder- und Jugendmedizin
Leiter, Experimentelle Pädiatrische Neurobildgebung
Universitäts-Kinderklinik
Abt. III (Neuropädiatrie)
Marko Wilke, MD, PhD
Pediatrician
Head, Experimental Pediatric Neuroimaging
University Children's Hospital
Dept. III (Pediatric Neurology)
Hoppe-Seyler-Str. 1
D - 72076 Tübingen, Germany
Tel. +49 7071 29-83416
Fax +49 7071 29-5473
[log in to unmask]
http://www.medizin.uni-tuebingen.de/kinder/epn/
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