Dear Bruce,

I was reading the dt_recon tutorial and also the tutorial for the DTI Basics and I am  very confused regarding how I should use my dt_recon in order to register my subjects on the CVS space and do a group study for FA and mean diffusivity.

1) I will be very grateful if you can confirm if my coding is write. First can you please let me know if by default dt_recon is re-sample FA to talairch space? In this case because I want to register   on CVS should I add the  --no-tal flag? I am asking this question because after I ran the following command I see in my  output directory called P07_dti a file called fa_tal.nii as well as fa_tal.nii.reg.

2) Do I need this files if I want to do a group study for my FA and mean diffusivity, similar to TBSS in FSL?

3) Can I use the talairch registration  or should I use the CVS?

4) Should I add the flag  --no-tal?

This is what I was running:

setenv FREESURFER_HOME /usr/local/freesurfer
setenv SUBJECTS_DIR $FREESURFER_HOME/subjects/DTI_FS/dtrecon

dt_recon --i P07_dti.nii.gz  -- b P07.bvals P07.bvects --s P07 --o P07_dti  where

P07_dti.nii.gz is my DTI volume

P07.bvals P07.bvects are the bvals and bvects for my subject

P07 is my structural recons data for my P07 subject

5) From the dt_recon --help I understand that dt_recon is doing the registration of lowb to same-subject anatomical using
   FSLs flirt (creates mask.nii and register.dat). 

mri_vol2vol --mov /usr/local/freesurfer/subjects/DTI_FS/dtrecon/P07_dti/lowb.nii \
            --targ $SUBJECTS_DIR/P07/mri/wmparc.mgz \
            --inv --interp nearest --o $SUBJECTS_DIR/P07/mri/wmparc2diff.mgz \
            --reg /usr/local/freesurfer/subjects/DTI_FS/dtrecon/P07_dti/register.dat --no-save-reg

6) Should I run mri_vol2vol  to re-sample the structural volume in the diffusion space and register in the CVS space:

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 /usr/local/freesurfer/subjects/DTI_FS/dtrecon/dti_15_p7/fa-masked.mgz \
            --o /usr/local/freesurfer/subjects/DTI_FS/dtrecon/dti_15_p7/fa-masked.ANAT+CVS-to-avg35.mgz \
            --interp trilin --no-save-reg

Thank you very much  for your time, your valuable explanations and help.

Antonella