Hi Freesurfers,
I was wondering if there was a way to save any configurations you make to
functional overlays (sig.mgh / sig.nii) in Tksurfer so you don't need to
change them again. When I go to View --> Configure --> Overlay, it seems
that the default is "Linear Opaque" with Min = 2.0 and Max = 5
I assume the label is a binary mask in MNI152? If so, use mri_label2vol
and spec the label as a segmenation, use
$FREESURFER_HOME/average/mni152.register.dat as the registration,
specify --invertmtx, and use the orig.mgz in fsaverage as the template.
I *think* this should work.
doug
mmoayedi
You can set the min, mid, and slope from the command-line with -fmin,
-fmid, and -fslope (it computes the max based on those 3).
The min and the max you can set with env variables, like:
setenv FS_TKFTHRESH 2
setenv FS_TKFMAX 3
this will apply to both tksurfer and tkmedit. Note that when the MA
The output has to be a volume (eg, nii or mgh), not a label. If you need
a label, run mri_cor2label on the output.
doug
Massieh Moayedi wrote:
> Hi Doug,
>
> I tried it, and it seems that it's working until the very last step.
>
> Here's the output I get:
>
> > $ mri_label2vol --seg
> '/storag
Hello,
As I understand it, the surface area measure is not a real surface
area measure. It is more a measure of how much the brain has to be
stretched in order to get into a common space. My question is that if
the cortical volume is calculated by multiplying the thickness and the
surface area (
The area maps do contain the actual surface area of each vertex with units of
mm^2. The problem is that the area at a given vertex depends on how many
vertices a given patch of
cortex was divided into, which is initially uniform but then varies
arbitrarily due
to topology correction, rend
The surface area is the actual area of the surface. I think you may be
thinking of the jacobian, which measures the amount of stretching needed
to register with the surface atlas. Total cortical volume is available
from the "header" of the aseg.stats file, and that is a surface-based
measure.
