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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