Dear all,


On the FS Tutorial/Diffusion the FA masked is defined as:
mri_mask $TUTORIAL_DIR/$subj/dtrecon/fa.nii \
         $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz \
         $TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgz
and when it follows the resampling on the CVS space I see:

mri_vol2vol --targ $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \
            --m3z $SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \  
            --noDefM3zPath --reg $TUTORIAL_DIR/$subj/dtrecon/register.dat \
            --mov $TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgz \
            --o $TUTORIAL_DIR/$subj/dtrecon/fa-masked.ANAT+CVS-to-avg35.mgz \
            --interp trilin --no-save-reg
with the following explanation: The '--interp' flag indicates the type of interpolation we want to use for our resampling. We are not using a segmented volume as an input so we use the default trilinear (trilin) interpolation option. If you wanted to resample a segmentation volume (such as wmparc or aseg) in CVS space, you would want to use the nearest neighbor (nearest) interpolation option.

I don't understand what exactly means: "We are not using a segmented volume as an input" since the fa-masked is defined using the wmparc2diff?

I understood there two  masking options: (option 1) using the  wmparc to guide my masking  or (option 2) if I want to do the masking based upon intensity values found in the fa image.
I am not sure how will be the best to define my FA-mask if I was running the CVS registration with the option --noaseg and also I want to do a group study and see if my Fa values increases or decreases in controls vs. patients. Can you please give me an advise?


 Also, I am not sure if I am mixing things or not but can I define my mask using the wmparc if I did the registration with the --noaseg option?



Many thanks.
Antonella