Hi Lilla,


Many thanks again for your help. In the mean time I checked with echo $FREESURFER_HOME and as I knew my $FREESURFER_HOME is /usr/local/freesurfer
Under this directory I have the subjects directory but here  unfortunately I am having the cvs_avg35/mri/norm.mgz.

1) Can you please help me find or get the the cvs_avg35/mri/norm.mgz? I saw online the same question was posted on June 2011 but there is no answer for the question online:

http://www.opensubscriber.com/message/freesurfer@nmr.mgh.harvard.edu/15506607.html


2) Since for my TBSS TBSS study was used by the TBSS the  nonlinear registration  FNIRT (is about 15 times faster than IRTK on FA data and possibly a little more 'accurate') I would like to use for a Tal space a non-linear talairach registration. Can you please give me some directions on  how I can do this? What is the default Tal registration (linear or non-linear) for dt_recon?

3) When dt_recon is  aligning  the diffusion data in the Tal space is in fact aligning the register.dat data (difussion data already aligned to the structural data) and the output is the fa-tal.nii.gz? If not why I need the register.dat file?


4) So by my understanding each subject will have a file called fa-tal.nii which in fact represents the subject's registration on the Tal-space? How about the mean diffusivity? I don't have only one file for this adc.nii. What if I want to do a non_FA values study on the tal space?

5) I understood that the 'registration.dat' file describes a rigid-body transformation from the diffusion to the structural space and in order  to resample the structural volume in the diffusion space, I will need to apply the inverse of this transformation to my input volumes and to use for this the 'mri_vol2vol':

mri_vol2vol --mov $TUTORIAL_DIR/$subj/dtrecon/lowb.nii \
            --targ $SUBJECTS_DIR/$subj/mri/wmparc.mgz \
            --inv --interp nearest --o $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz \
            --reg $TUTORIAL_DIR/$subj/dtrecon/register.dat --no-save-reg

Is the register.dat file created by this function mri_vol2vol?  I believe the registration between the diffusion and structural space (so the register.dat file) has already
been computed as part of the previous pre-processing step so while using the mri_vol2vol as above do I need to use the '--no-save-reg' flag as in the above example or the '--save-reg' flag?

6) To resample the diffusion data of one subject  in the CVS space do I need to run after dt_recon the mri_vol2vol as below?

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

Do I need to run the mri_cvs_registration on the structural data in order to get the above .m3z file 'combined_tocvs_avg35_elreg_afteraseg-norm.m3z' before I run the mri_vol2vol?

If I want to have my second registration step done in the Tal space not CVS space since after running dt_recon I am getting the fa-tal.nii.gz and the fa-masked.mgz
is this the equivalent file  to  fa-masked.ANAT+CVS-to-avg35.mgz (if I use the CVS space)? In this case I don't need to run the last mri_vol2vol command?
Sorry for asking so many questions but it is very confusing the online material.


Many thanks!
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: Tuesday, November 15, 2011 5:11 PM
Subject: RE:[Freesurfer] dt_recon registration


Hi Antonella,

> 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?

$FREESURFER_HOME is different from your $SUBJECTS_DIR. Could you double check?

> 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.

Are you referring to a linear or a non-linear talairach registration? It will be you who needs to decide which space to use for analysis. You would want all your data to be well aligned in that space in order to achieve a meaningful group comparison. The decision might also depend on in which space you want to report your final results in.

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

I am not familiar with your study, so it would be hard to say.

> 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?

dt_recon has two registration steps. One aligns the diffusion data (lowb) to the structural (registration.dat is the default name of the registration file) and the other aligns the diffusion data in the Tal space (the resampled fa file in that space is fa-tal). You can use both freeview and thregister to check the alignment of your volumes.

Lilla




> ___________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________
> 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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