Hi all,
Based on what Ziad said in his message I gave this a try yesterday evening.
I used the defaults from fsl which yielded these commands lines for the normalisation for the anatomical and functional respectively
/usr/share/fsl/bin/flirt -in /home/colmconn/mriAnalyses/mrUserGroupDemo/data/ts/ctrl/s1/s1.anat.nii -ref /usr/share/fsl/etc/standard/avg152T1_brain.hdr -out /home/colmconn/mriAnalyses/mrUserGroupDemo/data/ts/ctrl/s1/s1.anat.registered.nii -omat /home/colmconn/mriAnalyses/mrUserGroupDemo/data/ts/ctrl/s1/s1.anat.registered.mat -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 12 -interp trilinear
/usr/share/fsl/bin/flirt -in /home/colmconn/mriAnalyses/mrUserGroupDemo/data/ts/ctrl/s1/s1.allruns.ed.nii -ref /usr/share/fsl/etc/standard/avg152T1_brain.hdr -out /home/colmconn/mriAnalyses/mrUserGroupDemo/data/ts/ctrl/s1/s1.allruns.ed.registered.nii -omat /home/colmconn/mriAnalyses/mrUserGroupDemo/data/ts/ctrl/s1/s1.allruns.ed.registered.mat -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 12 -interp trilinear
You can see the difference in the before and after normalisation screen shots which I've attached.
I haven't tried mcflirt yet. I might give it a go later today.
Bye,
Colm.