and the papers describing the subcortical segmentation scheme are found
at the bottom of the main wiki page:
http://surfer.nmr.mgh.harvard.edu/fswiki
in the section 'subcortical segmentation'.
On Tue, 2007-11-13 at 15:17 -0500, Doug Greve wrote:
> Look in $FREESURFER_HOME/FreeSurferColorLUT.tx
Look in $FREESURFER_HOME/FreeSurferColorLUT.txt
doug
joel bruss wrote:
This is the last question that I have...sorry to keep bothering you
all. Is there a page on the FS wiki or is there a man page that
details the value of each sub-cortical parcel? I see that each masked
are has a value (1,
This is the last question that I have...sorry to keep bothering you
all. Is there a page on the FS wiki or is there a man page that
details the value of each sub-cortical parcel? I see that each masked
are has a value (1, 2, 3, etc.) but before I make assumptions about
which values correspond wit
Hi Joel,
both the .m3z (nonlinear) and the .lta (linear) are transforms from the
subject to the atlas coordinate system, but all the labeling is done in
the subject space, so you should be set.
cheers,
Bruce
On Tue, 13 Nov 2007, joel bruss
wrote:
Hello-
I'm running FreeSurfer v4.01on SUS
btw, you can have mri_vol2vol convert directly to analyze by using a
.img extension. But why use analyze?
joel bruss wrote:
Nick-
Doug wrote:
Try this:
mri_vol2vol --mov aseg.mgz --targ rawavg.mgz --o aseg-in-native.mgz
--regheader --interp nearest
doug
Sure
Nick-
Doug wrote:
>Try this:
>mri_vol2vol --mov aseg.mgz --targ rawavg.mgz --o aseg-in-native.mgz
>--regheader --interp nearest
>doug
Sure enough, this worked. What I mean by "norm" is the file
/mri/norm.mgz which gets created in the CA Normalize section of
recon-all. Mike was kind enough to
Joel,
All freesurfer volume files, including aseg.mgz, are in native MRI
space. The various talairach transforms are used to align to the
atlases used in freesurfer. I'm not sure what you mean by 'norm' space.
The --apply_transform flag of mri_convert can be used to convert a
volume to talairach
Try this:
mri_vol2vol --mov aseg.mgz --targ rawavg.mgz --o aseg-in-native.mgz
--regheader --interp nearest
doug
joel bruss wrote:
Hello-
I'm running FreeSurfer v4.01on SUSE Linux
I'm interested in viewing the sub-cortical parcels, /mri/aseg.mgz, but
in the native MRI space. I see that t
Hello-
I'm running FreeSurfer v4.01on SUSE Linux
I'm interested in viewing the sub-cortical parcels, /mri/aseg.mgz, but
in the native MRI space. I see that the output of "CA Label" produces
a file that is fit to the "CA Normalize" step but I can't figure out
the transform that was used. Specifi
