Hi Nazanin
1. The registration is only one step in how we do segmentation, so I
wouldn't suggest just using it. If you can convert your registration to
.m3z format and put it in the subjects transforms/talairach.m3z you could
try running from there forward.
2. Yes, you can edit the aseg in freeview.
3. Yes, the segmentations have improved in V6
cheers
Bruce
On Wed, 8 Nov 2017, N Saf
wrote:
Hi Bruce
as you explain I did the registration somewhere else and now I have the
labels_gca in my subject
space.
1. is it possible to somehow import this file in freesurfer and run the rest of
the analysis ?
2.my question in general is that : can I in anyway do any correction for aseg
outputs during the
analysis(similar to troubleshooting for surface-base analysis) e.g. do some
step with different
method and then import the result and use the rest steps in freesurfer??
3.Is there any difference between the subcortical segmentation results in v.6
vs v5.3 (except the
hippopotamus subfields segmentation which is available in v.6 . Is the hole
hippocampus volume
result different between 2 versions?)
I'm really appreciated for the help.
Best Regards,
Nazanin
On Mon, Oct 30, 2017 at 5:36 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
Hi Nazanin
the nonlinear registration is actually to our segmentation atlas (*.gca).
I guess you
could try using something else, but you should extract a mean intensity
image from the
gca as a target, not the MNI305. You can do this with:
mri_convert -nth 0 <file>.gca mean_gca.mgz
FYI, this:
mri_convert -nth 1 <file>.gca labels_gca.mgz
would give you the highest prior label at each spot (and 2 would give you
the prior)
cheers
Bruce
On Mon, 30 Oct 2017, N Saf wrote:
Dear Experts,
In the volume-based stream, if I'm right the FreeSurfer does two
registration with MNI305 ,one affine and one
nonlinear , is it possible to perform the nonlinear registration
somewhere
else and then use the result in
FreeSurfer and run the rest of the analysis ?
thank's alot for your great support.
BRG,
Nazanin
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