Dear Anders and Elizabeth,
The result of fslmeants will only give you intensity values or averages of these, not a measure of mutual information.
To get mutual information use flirt with the options "-cost mutualinfo -schedule $FSLDIR/etc/flirtsch/measurecost1.sch" and specify the -in and -ref images. Also use "-omat /dev/null" to suppress the output of the identity matrix (which you don't need/want).
The first value of the output line is the mutual information value, although it does not have certain constant terms calculated (as the registration doesn't require these terms) and so is only really useful for comparisons with other FLIRT values. I'm
afraid you'll have to use fslsplit and a loop to get the value for each image in a 4D input, as the flirt command only operates on the first image in a 4D input.
All the best,
Mark
Hi Anders,
You can use fslmeants with the --showall option and enter the one 3D volume as a mask.
Hope that helps!
Elizabeth
On Apr 21, 2013, at 11:01 PM, Anders Eklund wrote:
Dear experts,
is there any FSL function that calculates the mutual information between two volumes? Or even better, is there any function that takes one volume and one 4D dataset and returns a timeseries with the mutual information for each timepoint?
cheers,
Anders