Hi Folks,
When I convert and load images (from gelx, analyze,
or brik format), the contrast and brightness are way off. In some cases the
entire brain looks bright white. This creates a problem for segmentation edits
because when I adjust the contrast for the auxiliary image (mri/orig) the
Hi Brian
The tkmedit View-- Configure Brightness Contrast option allows you to
configure the main and/or aux volume(s) to your liking. I suppose you
could set an environment variable once you determine to which degree you
want the aux volume brightness reduced -- assuming this would be the
We've got 2 subjects where we've gotten a segment fail error reading
that the corpus callosum can't be found.
I've retransferred and remotion corrected them and I still get the same
error message when I segment them.
Any suggestions on how to fix this or to find the CC at this stage?
Many
Jill,
you may need to set this manually. it is described in the
FreeSurferGuide.pdf ~page 31 available at the FreeSurfer site. It
descirbes how to fix this within csurf.
you can also use the command mri_fill with the -C flag and the talairach
coords of the cc you want to use. run
Thanks. I overlooked the aux adustment for some reason. The environment
variable would be nice because my contrasts are off for every participant,
to varying extents. I suspect that the display contrast and brightness do
not impact the segmentation, etc. Although, I would like to confirm this.
Hi Brian,
You're right, the display contrast and brightness don't actually impact
the segmentation; it's just for visualization purposes.
Cheers!
Ev
On Tue, 13 Aug 2002, Brian C. Schweinsburg wrote:
Thanks. I overlooked the aux adustment for some reason. The environment
variable would be
[Brian]
Thanks. I overlooked the aux adustment for some reason. The environment
variable would be nice because my contrasts are off for every participant,
Are you running tkmedit from the command line or from csurf? If the
former, you can use a startup script to set the brightness and
