Hi Abid
you can run recon-all -make all -s ....
and that should do it (since the timestamp on the orig has changed)
cheers
Bruce
On Fri, 9 Aug 2013, Abid Qureshi wrote:
Hi Dr. Fischl,
I've changed the intensity on the orig.mgz files so that there is better
differentiation between white matter and gray matter. Then do I restart
recon-all after a certain step in the process? How does recon-all know to
use the newly modified orig.mgz file.
Thanks,
Abid
On Thu, Aug 8, 2013 at 9:54 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
Hi Abid
--scale specifies a floating point number to multiply each voxel
intensity by, so --scale 0.5 will make every intensity half as
much
cheers
Bruce
On Thu, 8 Aug 2013, aqure...@nmr.mgh.harvard.edu wrote:
When I looked at orig.mgz it is actually too bright. It's
very hard to
differentiate white and gray matter from how bright the
image is. Maybe
that is the root of the problem. I tried correcting it
with mri_convert
like this:
cp orig.mgz holder_orig.mgz
mri_convert --scale 3 holder_orig.mgz orig.mgz
But scale 2-5 all increase the brightness further, which
would probably
worsen the problem. I wasn't able to find how to decrease
brightness (or
increase contrast) in mri_convert --help. How would I
decrease the
brightness? It does not take negative numbers (like -3).
Thanks,
Abid
------------------
maybe try scaling up the orig.mgz then? I never really
understood why the
nu darkens it sometime. Alternatively you could scale up
the nu, but you
will have already lost dynamic range
------------------
The 001.mgz actually looks good in this case
(in terms of intensity) so
I'm not sure if it makes sense to scale it up
further. The problem is with
the nu.mgz being too dark. I'll try it out
though if you think it will
also work in this case.
- Abid
---------------
you could try using --scale <scale factor> to
scale the intensities of the
001.mgz up
---------------
Hi Dr. Fischl,
I had a couple subjects that
failed recon-all. Although the
error log
said
recon-all failed at mri_watershed
it looks like the root problem is
a
couple steps earlier, because the
nu.mgz looks too dark. This was
discussed in a previous thread
from 2008.
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07293.html.
You wrote, "p.s. are the 001.mgz
and 002.mgz dark? The orig.mgz?
Sometimes
nu_correct can create very dark
images, and there are some
switches you
can loo through to correct them.
Alternatively if it is the
001.mgz,
mri_convert has a scale option you
can use."
On my subject 001.mgz looks good
(there was no 002.mgz file). It is
only
nu.mgz that looks too dark. It
looks like the solution you gave
then was
for a problematic 001.mgz file,
but from your response it looks as
if
the
problem was nu.mgz the solution
would be different. What are the
switches
you can loop through to correct
the nu.mgz.
Thanks,
Abid
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