We do not label those (yet!)

On 4/13/2020 2:42 PM, Koustav Chatterjee wrote:

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Dear Sir,

I am afraid I am yet to find pedunculopontine nucleus and locus coeruleus in particular through FS dev versions of labelings volume.

Could you please help me out?

Best Regards,

KC

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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