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
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
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 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 brain imagesare
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
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 > > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Thank you so much, Sir
On Mon, Apr 13, 2020 at 1:45 AM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
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 CautionThank 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
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 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 brain imagesare
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
We do not label those (yet!)
On 4/13/2020 2:42 PM, Koustav Chatterjee wrote:
External Email - Use Caution
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 mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
*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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
they aren't released yet, but we are working on them On Tue, 14 Apr 2020, Koustav Chatterjee wrote:
External Email - Use Caution
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 > > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Douglas N. Greve -
Koustav Chatterjee