Thanks for the help! I was able to re-orient the data using FLIRT, and decided
to analyze each run separately, but I am still having trouble finding the stats
from each cluster. I know you showed me how to acquire a specfic cluster and
make a mask for the data using that, but I was wondering where one can find the
information on each voxel in numbers(i.e. a file containing the Zmax, etc. and
co-ordinates of each voxel). I apologize for the misunderstanding, and if you
could help me with this that would be great, thanks!
-Eric
Quoting Christian Beckmann <[log in to unmask]>:
> There is a file called cluster_mask_zstat* in the .feat directory that
> labels each voxel according to the cluster it belongs to, e.g. if
> there
> are 10 clusters in the zstat image, this file contains integer values
> from 0 to 10. You can easily check for the number of clusters using
> 'avwstats cluster_mask_zstatX -R'. This can be used to generate masks
> using 'avwmath' (both programs come with fsl)
>
> If you're interested in generating a 4D AVW file that only contains
> those voxels that are within cluster Y of the zstat image X, say, you
> would need to
>
> i) generate a mask from the cluster_mask_zstatX file :
> 'avwmaths cluster_mask_zstatX -mult -1 -thr -Y -mult -1 -thr Y
> mask_filename'
>
> ii) use this mask to threshold the 4D data :
> 'avwmaths filtered_func_data -mas mask_filename newdata_filename'
>
>
> newdata_filename then is a 4D AVW file of the same size as the
> original
> data where only voxels contained within cluster Y of zstatX have
> non-zero time course
>
>
> Christian F. Beckmann
> Address: Oxford University Centre for Functional
> Magnetic Resonance Imaging of the Brain,
> John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
> Email: [log in to unmask]
> http://www.fmrib.ox.ac.uk/~beckmann/
> Phone: +44(0)1865 222713 Fax: +44(0)1865 222717 Mob: +44(0)7980
> 691852
>
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