Dear Lilla,


Thank you very much for your valuable help.

I still have few more questions and I will appreciate  if you can further help me.

1) Why I don't have in my $FREESURFER_HOME/subjects the cvs_avg35/mri/norm.mgz? In my subjects directory I only have my subjects and nothing else. How can I get the  cvs_avg35/mri/norm.mgz?

2) Do you believe that for my subjects-all children ages 6-13 the results are gone be OK if I use the talairach registration and re-sampling? As I mentioned in my previous email I would like to do
a two-group study similar with TBSS so to do a statistical analysis on the FA and non_FA data such as mean diffusivity, to see if there are any clusters that may survive by multiple comparisons without any covariant.

3) Do you have any suggestion regarding which registration is better to be used for this study?

4) How I can check for each individual subject  if the registration worked out well if for example  I choose the talairach space?
Do I run:

tkregister2 --mov lowb.nii --reg register.dat --surf

or which file is in fact the registered data file? Is the fa-tal.nii.gz or the lowb.nii.gz? You mentioned that the default registration is on  talairch space and the I see on dt_recon tutorial

 that is also doing a registration of lowb to same-subject anatomical so I have two registration done when I run the dt_recon? 

Sorry I am very confused and I will very grateful if you can
 make this a little clear for me.

Many thanks for your time and help.

Best regards,
Antonella

From: Lilla Zollei <lzollei@nmr.mgh.harvard.edu>
To: Antonella Kis <atorok9@yahoo.com>
Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Sent: Monday, November 14, 2011 4:13 PM
Subject: Re: [Freesurfer] dt_recon registration


Hi Antonella,

> 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.

The talairach registration and re-sampling does take place by default, but that should not affect your further processing as the fa.nii file (in the native space) is not deleted from the directory. So you can either leave the default settings or you can also use --no-tal.

> 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?

Are you referring to the tal registration files? If you want to do the group study in the CVS spacem then you will not need the tal registration files.

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

Depends on where you want to do your analysis.

> 4) Should I add the flag  --no-tal?

You can. If you don't you just end up with two additional files.

> 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

Actually dt-recon now uses bbregister, but the output of this step is still register.dat. With the above you move the wmparc into the diffusion space.

> 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

With the above you are going to move your diffusion file (fa) into the CVS space (by implicitely combining a moprh moving the diffusion file to the structural space and then to the CVS space) and not resampling the structural volume in the diffusion space.

> 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?

It should be in $FREESURFER_HOME/subjects (as indicated above in your command --targ).

--Lilla
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