Dear Antao,
Check the recent archives with the subject "make_average_subject error?" and
the recent exchange with Nick. On Doug's advice, I added 'xv' to the
beginning of each make_average* script
So,
#!/bin/tcsh -efxv
Instead of #!/bin/tcsh -ef
This produced the output that allowed the freesurf
There is no any output when I add --echo.
Antao
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] Behalf Of Nick
> Schmansky
> Sent: Friday, October 07, 2005 3:04 PM
> To: Antao Du
> Cc: Freesurfer Mailing List
> Subject: Re: [Freesurfer] RE: make_average_surface
Brian,
Glad it worked. Clearly that portion of the script needs to be updated
for better compatibility.
The messages you are seeing (about nu_8_dxyz.mnc and COR-.info) can be
ignored, as they are not errors. In the newest dev release, these
messages have been suppressed, because they do not ind
Nick,
This appears to have done the trick. Make_average_subject ran and created
the surfaces. It echos the following error message many times, but I assume
this does not matter as it occurs with recon-all as well: INFO: Volume
/tmp/mritotal_9750/nu_8_dxyz.mnc cannot be found.
It also specifies the
Can you tell me which OS you are running?
Type:
cat /etc/redhat-release
and
uname -a
On Fri, 2005-10-07 at 15:00 -0700, Antao Du wrote:
> Hi, When I run make_average_surface --subjects AD1293 AD1297 AD1299 --out
> average_cn, it finished within 1 second without any output and any error
This is a puzzling problem. Unfortunately I don't have access to a FC4
system to try to recreate what you are seeing.
However, can you edit your make_average_subject/surface/volume scripts
to comment-out these lines (shown here with comment-out chars added):
#set n = `echo $argv | grep -e --help
This sounds like a problem I am having, The same script works fine on my
mac, but not on my FC4 machine. Here is the output, and a message I sent to
before.
I changed the flags to ³efxv² as Doug recommended, and here is the output
for make_average_subject, make_average_volume and make_average_sur
Add --echo to the command to print its activity, and then send me the
output.
On Fri, 2005-10-07 at 15:00 -0700, Antao Du wrote:
> Hi, When I run make_average_surface --subjects AD1293 AD1297 AD1299 --out
> average_cn, it finished within 1 second without any output and any error
> message. I don't
Hi, When I run make_average_surface --subjects AD1293 AD1297 AD1299 --out
average_cn, it finished within 1 second without any output and any error
message. I don't know what is wrong. Any helps there?
I have not updated my freesurface so I downloaded make_average_surface from
a post by Nick in Jul
hi Daniel-
i've encountered this before. see whta the value of fthresh is currently:
puts $fthresh
if it is an integer. add a decimal place to it:
set fthresh 1.0
you may have to check each of the following:
fthresh
fmid
fslope
thanks,
brian
On Fri, 7 Oct 2005, Daniel Goldenholz wrote:
Hell
Kristine,
I think the subcortical labeling step requires the NU files, so these
would have to be created for your old subjects. You can do this with:
recon-all -nuintensitycor -subjid
This will create the nu file (or files, if orig files are COR files).
No other files are touched (no edits los
I have a question about the current dev release - how different is the
new 'stable' release going to be different from it?
Probably not very different, but we are still working on a few critical
bug fixes, and adding some final touches to the GUI programs.
Can I start processing some brains u
Hello,
I was wondering if anybody has any insight into the best way to coregister
functionals with anatomicals in Freesurfer. I am looking for an automated
method of coregistration. I noticed the spm_coregister command, but I am
working with AFNI BRIK files, and I assume this requires Analyze for
Xander,
I haven't encountered this error message, and can't seem to track down
its origin. Is it possible to upgrade your 2003 version of freesurfer
to a newer version? If not, if you can email me the csurf file found in
the $FREESURFER/bin directory, I might be able to figure out the
problem.
Hello. I used paint-sess-new and surf-sess-new, and they opened a nice
overlay without trouble. When I selected the configure overlay command
from the menu, I get an error - 'error! expression didn't have a numeric
value'
The details are below. What can I do?
expression didn't have numeric va
I don't think it will matter.
Sunaina Fotedar wrote:
Dear all,
Would it be feasible to do a group analysis with the present developmental
release of freesurfer on the subjects which were individually analyzed on the
previous(old) version of freesurfer?
In other words, is the Group analys
Dear all,
Would it be feasible to do a group analysis with the present developmental
release of freesurfer on the subjects which were individually analyzed on the
previous(old) version of freesurfer?
In other words, is the Group analysis module of present version sensitive to
the version in w
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