12 Apr
2020
12 Apr
'20
4:13 p.m.
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:
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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 > > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer