That might be scanner coordinates or it might be that they just took
into account the voxel size but used some other coordinate system. Can
you find out exactly what the coordinate system is? I really need that
information before I can give you an answer.
doug
On 03/27/2012 07:58 PM, Johnson
Hi Johnson, try something like this:
mri_label2vol --seg tracts.nii --temp orig.mgz --o tracts-in-fs.nii --regheader
tracts.nii
doug
On 03/26/2012 03:29 PM, Johnson wrote:
OK
T1 space is the space acquired from the machine, original anatomical space
regards
JG
On 03/26/2012 2:25 PM,
And what coordinate system are the xyz in?
doug
ps. Please post questions to the list and not to me personally. Thanks!
On 03/27/2012 04:10 PM, Johnson wrote:
Hi
I have the tracts in (x,y,z) format not as an nii file
regards
JG
On 03/27/2012 11:25 AM, Douglas N Greve wrote:
Hi Johnson,
They are in the same coordinate system as the original T1 file supplied
to FS to generate the aparc+aseg file
JG
On 03/27/2012 4:41 PM, Douglas N Greve wrote:
And what coordinate system are the xyz in?
doug
ps. Please post questions to the list and not to me personally. Thanks!
On
Hi Johnson, can you be more specific? scanner coordinates? voxel
coordinates?
On 03/27/2012 06:20 PM, Johnson wrote:
They are in the same coordinate system as the original T1 file
supplied to FS to generate the aparc+aseg file
JG
On 03/27/2012 4:41 PM, Douglas N Greve wrote:
And what
from my understanding, scanner coordinates (i.e. considering the
resolution of each voxel)
regards
JG
On 03/27/2012 6:14 PM, Douglas N Greve wrote:
Hi Johnson, can you be more specific? scanner coordinates? voxel
coordinates?
On 03/27/2012 06:20 PM, Johnson wrote:
They are in the same
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
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
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
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
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
OK
T1 space is the space acquired from the machine, original anatomical space
regards
JG
On 03/26/2012 2:25 PM, Bruce Fischl wrote:
can you post to the list so others can answer? And can you clarify
what you mean by T1 space?
On Mon, 26 Mar 2012, Johnson wrote:
Hi
well, I had to transfer
Hi
This is Johnson, I am researcher at univ. of IL at chicago, I have a
question regarding freesurfer:
What is the transformation matrix that relates the freesurfer aparc+aseg
space to the aparc+aseg-in-rawavg space,
I am asking this question for the following reason:
I have white matter fiber
Hi Johnson
have you tried using bbregister for this? It should give you a
register.dat that you can use with mri_vol2vol to transform your diffusion
data into aparc+aseg space if you want.
cheers
Bruce
On Mon, 19 Mar 2012, Johnson wrote:
Hi
This is Johnson, I am researcher at univ. of IL
Hi Bruce
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
Hi
This is Johnson, I am researcher at univ. of IL at chicago, I have a
question regarding freesurfer:
What is the transformation matrix that relates the freesurfer aparc+aseg
space to the aparc+aseg-in-rawavg space,
I am asking this question for the following reason:
I have white matter fiber
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