Dear Lilla,
I solved the problem with my registration so now is working well but I will be very grateful if you can help me with the following questions:
For the DTI group analysis study I am interested to see any changes in the FA values within two groups: controls versus patients (children with epilepsy). As you suggested I introduced a white matter mask that will ensure that I am only considering diffusion values in the white matter and then also I did corrected for multiple comparison running mri_glmfit-sim with the option grf (as Doug recommend me).
My questions are:
1)How can I conclude if there is an increase and/or decrease in the FA values in one group (for example patients) versus another group (example controls). In other words what I can conclude regarding the FA values based on the GLM results: blue versus red clusters from the http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Diffusion (I don't see anymore the image with red and blue clusters posted on this website!)
2) If my fa-mask was defined using the wmparc2diff.mgz so is a segmentation volume, in order to resample this volume (wmparc or aseg) in CVS space, do I need to use the nearest neighbor (nearest) interpolation option instead of --interp trilin? What will be the difference and is the difference visible in the intensity or in another parameter such as a smoother registration?
Thank you very much and Happy New Year! Antonella