Hi I am using Freesurfer version 3.0.5 via Linux and I am trying to label
my results on tksurfer. I have already loaded the group descriptor file
and the overlay. I can visualize my results but when I click on these
specific reasons, it does not tell me where these areas lie. How do I go
about labe
You can do:
"recon-all -make all -s and it will run all the remaining steps
that have not been done or are out of date.
On Fri, 25 Jan 2008, Chris Watson wrote:
Hello,
While running recon-all on a subject, my machine logged me off for an
unrelated reason. It was stopped during -autorecon3
yes, you can give mris_inflate a -n option, where is 10 by
default. The average surfaces don't always inflate the same as the
individuals, but it's only for display so we've never tried very hard to
fix it.
cheers,
Bruce
On Fri, 25 Jan 2008, Nick Schmansky wrote:
You could use mris_infla
You could use mris_inflate to inflate it more if you prefer.
On Fri, 2008-01-25 at 14:10 -0800, XJ Kang wrote:
> Hi,
>
> I ran "make_average_subject" to get averaged volume and surface. The
> average inflated surface looks like "half-inflated", not like
> individual's fully inflated smooth surfac
Oops, I should have asked what version you were using.
The -make flag is not in v3.
Instead you can do:
recon-all -hemi rh -autorecon3 -nosphere -s
This will run just the right hemisphere through the rest of
-autorecon3. Doing -nosphere will skip the step before -surfreg which was
already co
The GSL_DIR and FSL_DIR outputs are no longer displayed (neither are
distributed with freesurfer, but FSL will get setup if FSL is installed
where FSLDIR is defined). I've updated the wiki to show the proper
output.
Do you have X11 installed? Including the X11 updates from Apple? You
could also
Hi Juergen,
we haven't used 7T for surface recons, just for hires partial brain
studies. The dielectric effects are pretty severe, which may be causing
your problem. Can you get whole brain 1mm data as well as the hires data?
You can use the "conform to min" option (I can't remember what it is
As a final note on this, I have found an alternative way of creating
.mgh overlay files with multiple frames from data in matlab. Some test
reveal that writing out a data matrix of approx. 14x1x1x400 in size
takes >2gb memory and quite a long time (at least on my machine) in
Matlab. To avoi
Our neuroimaging lab at Brigham and Women's Hospital (Boston) is seeking
a part-time (20 hrs/week) post-doc to come join our group and assist in
human MRI analysis and post-processing. This individual will take a
lead role in the analysis of structural and diffusion tensor MRI studies
in an HI
I have just installed the Mac OS X version 4.0.2 for PowerPC. Everything
installed fine, but I have encountered errors beginning when I run the
script file. When running the script, I get the following message:
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /applicat
One option is:
recon-all -s (subj) -make all
The other is to follow this table and include just the flags for the
uncompleted stages:
http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
but it sounds like all you need is:
recon-all -s (subj) -autorecon3 -hemi rh
which you could follo
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