Hi Mike,
it is used a bit in mri_fill I think, although it might actually have
been removed now that we use the aseg. There is also the option of using
it to initialize the spherical morph, but that is disabled by default, so
it's not used very much. Generally as long as it's not dramatically
Mike,
I think it is perfectly acceptable to use the talairach.xfm file
generated for a subject by v4 for use with v3.0.5 processing. There is
no difference in the file format, it is just more accurate. Another
feature in v4 is a check of the talairach.xfm file against a set of
known-good alignme
Yes, based on a small N, version 4 does seem much more robust.
So, if we wanted accurate .xfm's without requiring manual editing, would
it be appropriate/fair to use v4 for autorecon1, but then use v3.0.5 for
autorecon2 and 3, so as to maintain compatibility with other data
processed under v3?
t
Is talairach.xfm even used as input for any stage of autorecon2 or 3?
(Or, is it just the talairach.lta and talairach.m3z files?)
thanks,
Mike H.
On Thu, 2007-10-11 at 16:28 -0400, Doug Greve wrote:
> It is not that important from a recon standpoint. However, if you intend
> to report talairac
William,
Freesurfer v3.0.5 is available for download from here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/stable/centos4_x86_64
Would it be possible for you to create a tarball of that subject and
send it to me? I would like to try to recreate the problem here (as I
am not
you could just rerun the tals with version 4 if you want.
On Fri, 12 Oct
2007, Michael Harms wrote:
Yes, based on a small N, version 4 does seem much more robust.
So, if we wanted accurate .xfm's without requiring manual editing, would
it be appropriate/fair to use v4 for autorecon1, but the
Hi,
I am trying to run an fMRI gamma analysis and am running into memory
problems. I'm running freesurfer version stable 4.0 on unix through
multnomah. The subject directory is located in
/space/multnomah/3/users/gow/PROZ06/MRI/PROZ06004. We're running into
issues with the selxavg-sess comman
The --paired-diff options just take the difference between adjacently
specfied inputs. You then set up your design matrix or FSGD file and
then run mri_glmfit. The --help for mri_glmfit has a lot of info about
the glm analysis. If you just want to test whether the difference is 0,
you can use
You're probably going to need a computer with more memory. That one only
has 1G.
doug
[EMAIL PROTECTED] wrote:
Hi,
I am trying to run an fMRI gamma analysis and am running into memory
problems. I'm running freesurfer version stable 4.0 on unix through
multnomah. The subject directory is l
Hi Chuck,
is that partition full?
Bruce
On Fri, 12 Oct 2007, Chuck Theobald wrote:
Hi,
Following some system upgrade to our Linux 2.6 systems, freesurfer has ceased
to work. When running recon-all on bert, we get a message referring to a
broken pipe and a crash in mincinfo. We are running G
Hi,
Following some system upgrade to our Linux 2.6 systems, freesurfer has
ceased to work. When running recon-all on bert, we get a message
referring to a broken pipe and a crash in mincinfo. We are running Gentoo:
doolin ~ # uname -a
Linux doolin 2.6.21-gentoo-r4 #1 SMP Thu Aug 9 09:33:11 PD
you might check the MNI list to see if this is a known issue for them.
On
Fri, 12 Oct 2007, Chuck Theobald wrote:
Hi,
No, we have sufficient disk space on each machine.
This used to work, but started failing following upgrades to system files. I
suspect libc.so.6 or libm.so.6, since mincin
Chuck,
Which freesurfer is installed? The rh9 freesurfer dist is built against
libstdc++.so.5 (which many systems dont have), whereas the centos
freesurfer dist uses .6.
Nick
On Fri, 2007-10-12 at 14:13 -0700, Chuck Theobald wrote:
> Hi,
>
> No, we have sufficient disk space on each machine.
>
Hi,
No, we have sufficient disk space on each machine.
This used to work, but started failing following upgrades to system
files. I suspect libc.so.6 or libm.so.6, since mincinfo is linked to
both, and both were part of the upgrade, but I don't have anything
specific pointing to this as the c
I believe we are using the CentOS version. I am downloading the RH9
distro for version 3.0.3 to see if that will work for us.
Chuck
Nick Schmansky wrote:
Chuck,
Which freesurfer is installed? The rh9 freesurfer dist is built against
libstdc++.so.5 (which many systems dont have), whereas the
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