Sebastian,
I've attached a gzipped recon-all that has the -noseg flag. Do not copy
over the recon-all in your 2005-10-03 release, as it's not fully
compatible with that. Rather, I suggest opening the new recon-all in a
text editor, and look for instances of the variable 'UseAseg', and the -
noas
Hi Nick, hi All,
On 22. Feb 2006, at 19:39 Uhr, Nick Schmansky wrote:
In the freesurfer dev releases post 2006-18-01, there is a -noaseg flag
in recon-all. It will skip the auto-segmentation step, and not include
aseg.mgz in any subsequent processing (eg. wm seg and filling). The
flag is inte
In the freesurfer dev releases post 2006-18-01, there is a -noaseg flag
in recon-all. It will skip the auto-segmentation step, and not include
aseg.mgz in any subsequent processing (eg. wm seg and filling). The
flag is intended for usage with baby brains and non-human primates, as
these brains ca
Dear all,
at the moment I am struggling with flattening monkey anatomical scans.
Specifically I manually got to the point where I get a wm.mgz and now I
want to inflate it. My instructions refer to using csurf, which does
not like my mgz volumes and is deprecated IIRC, the alternative is
hook
I don't think so.
Glenn Lawyer wrote:
Hi,
We like to structure our work by putting all scans into a batch account
and doing recon-all -autorecon1 -autorecon2. We then transfer the scans
to our individual accounts to check the quality before running the rest
of the processing stream.
Hi Darren and other Freesurfers
I wrote a tcl script to do just what was described. The one I made gives
the flexibility to name the tiff files based on a prefix that you
specify before
running the script. This way you run the same exact script for as many
pictures as you like, simply changing
If you are using a recent dev version of tksurfer, then try the function:
save_tiff
If you enter this into the shell and it doesn't work, then you have an
older version. Our new release will have this function.
There is (finally) some documentation for scripting commands in
tksurfer, although
Hi,
We like to structure our work by putting all scans into a batch account
and doing recon-all -autorecon1 -autorecon2. We then transfer the scans
to our individual accounts to check the quality before running the rest
of the processing stream.
This creates a small problem, in that the full
Marcus,
You may want to try the centos4 build of freesurfer. It is built
against libstdc++.so.6, whereas the rh9 build builds against libstdc+
+.so.5.
I don't know whether this would account for the partial brain you are
seeing, or why, but its worth a try.
Nick
On Wed, 2006-02-22 at 10:58 +0
Hi, Darren,
I once made an animated gif of a rotating brain showing some freesurfer
results. I did this with two scripts. The first is a tcl script that
was passed to tksurfer; it rotates the brain and saves the resulting
images. The second is a shell script that uses imagemagik to convert
all
is that the orig surface? Usually that's what is displayed in green (the
white is in yellow). This kind of thing usually means an incorrectly fixed
topological defect, so the best bet is to manually correct the defect.
Bruce
On Wed, 22 Feb 2006, Martin Ystad wrote:
Hi, I've just installed the
Dear all,
does someone out there run freesurfer
(freesurfer-Linux-rh9-dev20060210-full.tar.gz) under debian etch?
Installation runs smoothly, however, when I test the freesurfer
installation with
medpc32:~$ tksurfer bert rh pial
only a tiny fraction of Bert's brain is displayed. The GUI otherwis
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