you could try using --scale <scale factor> to scale the intensities of the
001.mgz up
On Wed, 7
Aug 2013, Abid Qureshi wrote:
I'm using 4.5.0. The earliest subjects were done using 4.5.0 so for consistency
we are sticking with 4.5.0. -
Abid
On Wed, Aug 7, 2013 at 6:52 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote:
Hi Abid
what version of FS are you using?
Bruce
On Wed, 7 Aug 2013, aqure...@nmr.mgh.harvard.edu wrote:
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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