Dhruman
Thanks for catching that. Spelling was never my strong point. I have
corrected the script on my website.
As for you second problem, did you properly remove the waitfor
step1-00.done from the motion correction step, since you
say you skipped step1-00, i.e. the invol step? I mention thi
Hi Eli,
the eTIV is estimated from the talairach_with_skull.lta linear transform,
so you might visually verify that it is correct on our subjects.
chers,
Bruce
On Tue, 21
Mar 2006, Eli Diamond wrote:
Hello,
I'm writing because I am trying out some structure-function analyses and I
woul
Hi Daniel,
I was having a second look at the script and apparently the script is
fine with a small spelling error. The STAT variable which is set at 3
different instances has spelling error in "scripts" where "t" is
missing.
Once this was corrected the script is fine but it's still not working.
It
Hi,
I have been working with an image dataset of EPI
images and MR images that have been registered in the freesurfer (transformation
for which is stored in a .reg file).
A T1 mgz volume was made using the following
command:
mri_convert -it analyze -ot mgh -i T1001.img -o T1.mgz
I form
Hi Eliz,
you're better of using stable for exactly this reason - we've tested it
extensively and it works quite well. Dev is on the other hand definitely
*not* stable.
Bruce
On Tue, 21 Mar 2006, Elizabeth Fenstermacher wrote:
Hey Bruce,
I had been using the dev environment, but I'm rerunn
Hey Bruce,
I had been using the dev environment, but I'm rerunning them now in the
stable per Nick's suggestion.
I didn't realize that it was an established, if relatively new, bug
because I hadn't had problems before.
Eliz
On Tue, 21 Mar 2006, Bruce Fischl wrote:
what version are you u
Hello,
I'm writing because I am trying out some structure-function analyses and I
would like to normalize my label volume measurements with the total
intracranial volume. I was informed that this value is in
/stats/aseg.stats.
I was surprised at the range of TIVs that I saw in my 29 subjects
what version are you using?
On Tue, 21 Mar 2006, Elizabeth Fenstermacher
wrote:
Yes that's exactly what's happening. Well I'm sorry to hear that this is
endemic now :(, but I'm glad I'm not crazy ...
On Tue, 21 Mar 2006, Bruce Fischl wrote:
Hi Eliz,
are they faulting in the middle of
There is a known bug in the dev environment (at the NMR center).
It is recommended to use the stable environment:
source /usr/local/freesurfer/nmr-std-env
On Tue, 2006-03-21 at 14:16 -0500, Elizabeth Fenstermacher wrote:
> Hey All,
>
> I have a few scans that I've been attempting to process
Hi Eliz,
are they faulting in the middle of mri_ca_register? We've just started to
have this problem (despite successfully running it on our 80 hemisphere
test set!), and I'm tracking it down.
sorry :<
Bruce
On Tue, 21 Mar 2006,
Elizabeth Fenstermacher wrote:
Hey All,
I have a few sca
Yes that's exactly what's happening. Well I'm sorry to hear that this is
endemic now :(, but I'm glad I'm not crazy ...
On Tue, 21 Mar 2006, Bruce Fischl wrote:
Hi Eliz,
are they faulting in the middle of mri_ca_register? We've just started to
have this problem (despite successfully runni
Hey All,
I have a few scans that I've been attempting to process that fail during
autorecon2. I've eliminated all scan acquisitions that looked potentially
problematic and attempted to rerun them. They both seem to go through
autorecon1 without incident. The errors I'm getting are the some
That was it. Thanks so much. Just added the unsetenv line to my .cshrc
file.
Cliff
--
Clifford Smith, PhD
Assistant Professor of Behavioral Sciences
Rush University Medical Center
312.942.2893
> From: Nick Schmansky <[EMAIL PROTECTED]>
> Date: Tue, 21 Mar 2006 12:28:43 -0
Clifford,
After sourcing SetUpFreeSurfer.csh, but before starting FSL, type this:
unsetenv TCLLIBPATH
This should take care of the problem you are seeing. You may want to
include that line in your SetUpFreeSurfer.csh file.
Nick
On Tue, 2006-03-21 at 10:36 -0600, Clifford A. Smith, PhD wrote
Hi - I suspect that the simplest solution is to source the FreeSurfer
setup _before_ the FSl setup.
Cheers, Steve.
On 21 Mar 2006, at 16:36, Clifford A. Smith, PhD wrote:
I believe that I have read a post on this in the past, but I was
unable to run a search. I have FSL configured to start
Title: FSL/Freesurfer
I believe that I have read a post on this in the past, but I was unable to run a search. I have FSL configured to startup in X11 without a problem. Also can run Freesurfer (source SetupFreeSurfer.csh) without a problem. But FSL will not work after I have ran the source S
Hi, I'm using stable 3.0 with the recon-all -all command (so whichever atlas is
the default for lh.aparc.annot). I'm not sure if this is what your 2nd question
is asking, but the pial outlines do tend to "cross under" the orig slightly (as
shown above). I kind of assumed this was normal though.
Hi Aaron,
don't bother looking at the orig - look at the white and pial instead.
The pial in your image looks fine.
Bruce
On Tue, 21 Mar 2006, Goldman, Aaron
(NIH/NIMH) [C] wrote:
Hi, I'm using stable 3.0 with the recon-all -all command (so whichever atlas is the
default for lh.aparc.anno
Hello Bruce and all,
Is it possible to perform group analysis based only on a particular
subcortical region of interest and visualize it?
-Dhruman
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Bruce
Fischl
Sent: Monday 20 March 2006 16:20
To: Shahabuddi
depends what you mean. You can do group analysis of structure volumes, but
visualizing that is a matter of bar charts and such. We also have some
tools for making "density" measures, but those aren't integrated into the
distributed version yet.
cheers,
Bruce
On Tue, 21 Mar 2006, Goradia, Dhru
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