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*Thank you Sir for your reply.*
On Tue, Apr 14, 2020 at 12:20 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
We do not label those (yet!)
On 4/13/2020 2:42 PM, Koustav Chatterjee wrote:
External Email - Use CautionDear 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 CautionDear 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 brainimages 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 tractsin
Freesurfer?Thank you for your time and effort. Regards, Koustav
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