Hi Johnson - The aparc+aseg.mgz is in the same space as the T1 used as input to freesurfer.
a.y
On Mon, 26 Mar 2012, Johnson wrote:
Hi FS expert I need to know the transformation matrix itself since I will do the transformation in matlab. I successfully transformed white matter fibers coordinates to T1 using AIR 5.0 from LONI lab. They provide a transformation matrix. Now I want to transform the coordinates from T1 to Freesurfer space, so my question is: what is the transformation matrix that relates the T1 which FS have used for parcellation and segmentation with the aparc+aseg.mgz file? I searched the logs but couldn't find such matrix. I don't want to do a registration step since it will be less accurate than the one that was generated during the segmentation process. Also is it just one transformation or a combination of transformations?
thanks
Hi I found it in a 256x256x256 space while the T1 we use is in different space, I found this page on the registration step: http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat I wish to know how this script work?
mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --regheader aseg.mgz
what is the transformation used ? JG
On 03/26/2012 12:24 PM, Anastasia Yendiki wrote:
Hi Johnson - The aparc+aseg.mgz is in the same space as the T1 used as input to freesurfer.
a.y
On Mon, 26 Mar 2012, Johnson wrote:
Hi FS expert I need to know the transformation matrix itself since I will do the transformation in matlab. I successfully transformed white matter fibers coordinates to T1 using AIR 5.0 from LONI lab. They provide a transformation matrix. Now I want to transform the coordinates from T1 to Freesurfer space, so my question is: what is the transformation matrix that relates the T1 which FS have used for parcellation and segmentation with the aparc+aseg.mgz file? I searched the logs but couldn't find such matrix. I don't want to do a registration step since it will be less accurate than the one that was generated during the segmentation process. Also is it just one transformation or a combination of transformations?
thanks
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
If you want to register your DWI to T1, you should register to mri/brain.mgz. You can do this with bbregister, or with any affine registration tool of your choice.
On Mon, 26 Mar 2012, Johnson wrote:
Hi I found it in a 256x256x256 space while the T1 we use is in different space, I found this page on the registration step: http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat I wish to know how this script work?
mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --regheader aseg.mgz
what is the transformation used ? JG
On 03/26/2012 12:24 PM, Anastasia Yendiki wrote:
Hi Johnson - The aparc+aseg.mgz is in the same space as the T1 used as input to freesurfer.
a.y
On Mon, 26 Mar 2012, Johnson wrote:
Hi FS expert I need to know the transformation matrix itself since I will do the transformation in matlab. I successfully transformed white matter fibers coordinates to T1 using AIR 5.0 from LONI lab. They provide a transformation matrix. Now I want to transform the coordinates from T1 to Freesurfer space, so my question is: what is the transformation matrix that relates the T1 which FS have used for parcellation and segmentation with the aparc+aseg.mgz file? I searched the logs but couldn't find such matrix. I don't want to do a registration step since it will be less accurate than the one that was generated during the segmentation process. Also is it just one transformation or a combination of transformations?
thanks
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Let me re-phrase my question: I already did registration from DWI to T1, this step is OK. Now I want to go from T1 to FreeSurfer space (aparc+aseg.mgz file not the aparc+aseg-in-rawavg file). I know I have two choices: 1) do registration using bbregister 2) since Freesurfer during processing have already done this step, the transformation matrix is there somewhere, the question is where to find it? which log or which file? this choice is better since it is more accurate.
Thanks JG
On 03/26/2012 12:41 PM, Anastasia Yendiki wrote:
If you want to register your DWI to T1, you should register to mri/brain.mgz. You can do this with bbregister, or with any affine registration tool of your choice.
On Mon, 26 Mar 2012, Johnson wrote:
Hi I found it in a 256x256x256 space while the T1 we use is in different space, I found this page on the registration step: http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat I wish to know how this script work?
mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --regheader aseg.mgz
what is the transformation used ? JG
On 03/26/2012 12:24 PM, Anastasia Yendiki wrote:
Hi Johnson - The aparc+aseg.mgz is in the same space as the T1 used as input to freesurfer.
a.y
On Mon, 26 Mar 2012, Johnson wrote:
Hi FS expert I need to know the transformation matrix itself since I will do
the > transformation in matlab.
I successfully transformed white matter fibers coordinates to T1
using > AIR 5.0 from LONI lab.
They provide a transformation matrix. Now I want to transform the coordinates from T1 to Freesurfer
space, so
my question is: what is the transformation matrix that relates
the T1
which FS have used for parcellation and segmentation with the >
aparc+aseg.mgz file?
I searched the logs but couldn't find such matrix. I don't want to do a registration step since it will be less
accurate > than the one that was generated during the segmentation process.
Also is it just one transformation or a combination of
transformations?
thanks
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Actually, (1) should be more accurate, because bbregister uses the surface reconstruction obtained from the T1 to optimize the contrast across the gray/white boundary in the registered DWI.
However if you want to convert to the 1mm, 256^3 voxel size that was used as input to freesurfer, see mri_convert --conform.
On Mon, 26 Mar 2012, Johnson wrote:
Hi Let me re-phrase my question: I already did registration from DWI to T1, this step is OK. Now I want to go from T1 to FreeSurfer space (aparc+aseg.mgz file not the aparc+aseg-in-rawavg file). I know I have two choices:
- do registration using bbregister
- since Freesurfer during processing have already done this step, the
transformation matrix is there somewhere, the question is where to find it? which log or which file? this choice is better since it is more accurate.
Thanks JG
On 03/26/2012 12:41 PM, Anastasia Yendiki wrote:
If you want to register your DWI to T1, you should register to mri/brain.mgz. You can do this with bbregister, or with any affine registration tool of your choice.
On Mon, 26 Mar 2012, Johnson wrote:
Hi I found it in a 256x256x256 space while the T1 we use is in different space, I found this page on the registration step: http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat I wish to know how this script work?
mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --regheader aseg.mgz
what is the transformation used ? JG
On 03/26/2012 12:24 PM, Anastasia Yendiki wrote:
Hi Johnson - The aparc+aseg.mgz is in the same space as the T1 used as input to freesurfer.
a.y
On Mon, 26 Mar 2012, Johnson wrote:
Hi FS expert I need to know the transformation matrix itself since I will do
the > transformation in matlab.
I successfully transformed white matter fibers coordinates to T1
using > AIR 5.0 from LONI lab.
They provide a transformation matrix. Now I want to transform the coordinates from T1 to Freesurfer
space, so
my question is: what is the transformation matrix that relates
the T1
which FS have used for parcellation and segmentation with the >
aparc+aseg.mgz file?
I searched the logs but couldn't find such matrix. I don't want to do a registration step since it will be less
accurate > than the one that was generated during the segmentation process.
Also is it just one transformation or a combination of
transformations?
thanks
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Johnson
what T1 did you register to? Most of the ones we generate (T1.mgz, brainmask.mgz, ...) are in a common coordinate system and you shouldn't have to transform from one to another. cheers Bruce
On Mon, 26 Mar 2012, Johnson wrote:
Hi Let me re-phrase my question: I already did registration from DWI to T1, this step is OK. Now I want to go from T1 to FreeSurfer space (aparc+aseg.mgz file not the aparc+aseg-in-rawavg file). I know I have two choices:
- do registration using bbregister
- since Freesurfer during processing have already done this step, the
transformation matrix is there somewhere, the question is where to find it? which log or which file? this choice is better since it is more accurate.
Thanks JG
On 03/26/2012 12:41 PM, Anastasia Yendiki wrote:
If you want to register your DWI to T1, you should register to mri/brain.mgz. You can do this with bbregister, or with any affine registration tool of your choice.
On Mon, 26 Mar 2012, Johnson wrote:
Hi I found it in a 256x256x256 space while the T1 we use is in different space, I found this page on the registration step: http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat I wish to know how this script work?
mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --regheader aseg.mgz
what is the transformation used ? JG
On 03/26/2012 12:24 PM, Anastasia Yendiki wrote:
Hi Johnson - The aparc+aseg.mgz is in the same space as the T1 used as input to freesurfer.
a.y
On Mon, 26 Mar 2012, Johnson wrote:
Hi FS expert I need to know the transformation matrix itself since I will do
the > transformation in matlab.
I successfully transformed white matter fibers coordinates to T1
using > AIR 5.0 from LONI lab.
They provide a transformation matrix. Now I want to transform the coordinates from T1 to Freesurfer
space, so
my question is: what is the transformation matrix that relates
the T1
which FS have used for parcellation and segmentation with the >
aparc+aseg.mgz file?
I searched the logs but couldn't find such matrix. I don't want to do a registration step since it will be less
accurate > than the one that was generated during the segmentation process.
Also is it just one transformation or a combination of
transformations?
thanks
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
-
Anastasia Yendiki -
Bruce Fischl -
Johnson