yes, if you run your T1 through FreeSurfer's recon-all you should be able
to use tracula afterwards to reconstruct tract models from your dwi data.

We use T1 because it is by far the most common anatomical sequence and
historically has had better cnr/unit-time

cheers
Bruce

On
Mon, 13 Apr 2020, Koustav Chatterjee wrote:

>
>         External Email - Use Caution        
>
> Thank you very much Sir for your effort and time to answer my questions.
> I am afraid I have not got the answer for the following:
>
>  *  If I have Freesurfer installed in my PC; I also have T1 and diffusion
>     weighted image sequence of a subject. Can I use 'Tracula' to analyse
>     tracts of that subject's brain directly? How could I analyse tracts in
>     Freesurfer?  
>
> It would also be kind enough why T1 weighted or T2 can only be read by
> FreeSurfer? Is this because of the algorithm they use.
>
> On Sun, Apr 12, 2020 at 10:46 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu>
> wrote:
>       Hi Koustav
>
>       the current version of FS requires a T1-weighted input but could
>       also use
>       a T2 to improve accuracy and automaticity. Future versions will
>       relax
>       this constraint.
>
>       As for 2D/3D, you have to distinguish the acquisition type
>       (which almost
>       always should be a 3D sequence like an MP-RAGE or a 3D
>       FLASH/SGPR) from
>       the model. When we say "2d cortical surface" we are talking
>       about
>       extracting that model ("reconstructing" it) from the 3D data
>
>       As for the structures you mention, we have dev versions of
>       labelings for
>       all of them I believe, but I defer to Doug on the details
>
>       cheers
>       Bruce
>
>
>       On Sun, 12 Apr 2020, Koustav Chatterjee wrote:
>
>       >
>       >         External Email - Use Caution        
>       >
>       > Dear all,
>       > I am a beginner in FreeSurfer world.
>       > I have 4 questions. It would be kind enough if you could
>       clarify my
>       > confusions.
>       >  *  I have came across that 'Freesurfer can reconstruct 2D
>       cortical surface
>       >     from 3D T1 MRI brain image'. However, I know that T1 2D
>       brain images are
>       >     being fed to freesurfer for 'Recon-all...-all' to function
>       all its
>       >     pre-processing steps. 
>       > Whether ".......reconstruct 2D cortical surface from 3D T1 MRI
>       image" this
>       > statement is true? Is there any step where FreeSurfer make a
>       3D image from
>       > 2D T1 images and again reconstruct them into 2D
>       > cortical surface through preprocessing steps?
>       >
>       >  *  Can FreeSurfer only recognize 'T1 weighted images' for
>       processing? Why
>       >     only T1, why not T2 or Flair etc?
>       >  *  Can we estimate the volume of substantia nigra,
>       pedunculopontine nucleus
>       >     and locus cereleus using FreeSurfer? If so any specific
>       version
>       >     of Freesurfer is required?
>       >  *  If I have Freesurfer installed in my PC; I also have T1
>       and diffusion
>       >     weighted image sequence of a subject. Can I use 'Tracula'
>       to analyse
>       >     tracts of that subject's brain directly? How could I
>       analyse tracts in
>       >     Freesurfer?
>       > Thank you for your time and effort.
>       > Regards,
>       > Koustav
>       >
>       >
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