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
7) I found online that the default CVS template is cvs_avg35 which is supplied with my FreeSurfer distribution. Can you please tell me in which directory is located or how I can obtain the cvs_avg35?
Thank you very much for your time, your valuable explanations and help. Antonella