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?

When you masked the FA volume, you eliminated some values that are outside of the mask but did not create a binary volume, the original FA values remained in the volume.

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?

These two things are not related. When considering the masking the only thing you need to think about is whethe ryou trust the parcellation map or an intensity threshold better in order to define voxels that you would like to keep in your input volume.

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?

Again, these deceisions are not related.

Lilla