orig.mgz is not converted to Talairach. The computed Talairach xfm is
used internally by some stages of recon-all, but none of the volumes are
ever converted to Talairach/MNI space.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for
Hi Harm,
Thanks for the trick. Will this, however, give not rise to conversion to
Talairach
coordinates?
Cheers,
Ed
On 6 Feb 2014, at 15:38, Harms, Michael wrote:
>
> Hi Ed,
> If you want to avoid the rotation (e.g., to avoid an interpolation at the
> conform step) then you need to manually
Hi Ed,
If you want to avoid the rotation (e.g., to avoid an interpolation at the
conform step) then you need to manually alter the input so as to remove
the off-diagonal elements. That is in fact what we do as part of our
DICOM2NIFTI conversion in the HCP.
cheers,
-MH
--
Michael Harms, Ph.D.
-
Hi Bruce,
Yes, I do understand that is coronal, but there is an actual rotation apart
from an orientation to coronal.
You can read it from the off-diagonal matrix elements.
Cheers,
Ed
On 6 Feb 2014, at 14:36, Bruce Fischl wrote:
> yes, we reorient it to be coronal as part of the "conform" proc
yes, we reorient it to be coronal as part of the "conform" process
cheers
Bruce
On Thu, 6
Feb 2014, Ed Gronenschild wrote:
> Hi,
>
> Using recon-all (freesurfer v5.1.0, MacOSX10.6) I noticed a rotation
> of the T1 data early in the pipeline, i.e., converting rawavg.mgz to
> orig.mgz., see excerp
Hi,
Using recon-all (freesurfer v5.1.0, MacOSX10.6) I noticed a rotation
of the T1 data early in the pipeline, i.e., converting rawavg.mgz to
orig.mgz., see excerpt of output of mri_info below
rawavg.mgz:
xform info: x_r = 0.0081, y_r = -0.0913, z_r = 0.9958, c_r = 0.0813
