check the aseg and see if it's reasonable. Something is badly wrong if
there are no lh and rh white matter points that are nbrs.
cheers,
Bruce
On Fri, 6 Jan
2006, Fornito, Alexander wrote:
Hi,
I've been getting the following error message when running autorecon2-wm with
some of my images.An
hi again
we've been trying various things to get mk-fieldsign to work: installing the
development version of freesurfer and trying it on a different computer, but we
get the same error message. We thought that perhaps mk-fieldsign doesn't have
the same access permissions as the other tcl scripts o
Hi, I downloaded the new version of
mris_convert, but I’m having trouble getting it to run successfully. When
I start with bfloats it says freadFloat: fread failed a bunch of times, and starting
with a COR file it says it can’t allocate memory. How do I specify the mgh
format you recommende
what was your command-line? For mris_glm, specify --beta beta.mgh. btw,
the rvar output will be the variance of the thickness.
Goldman, Aaron (NIH/NIMH) [F] wrote:
Hi, I
downloaded the new version of
mris_convert, but I’m having trouble getting it to run successfully.
When
I sta
Hi Jane,
Can you send all the relevant info? See
https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
doug
Jane Aspell wrote:
hi again
we've been trying various things to get mk-fieldsign to work: installing the
development version of freesurfer and trying it on a different computer
use mri_convert, not mris_convert (the version with the "s" is for
surfaces, not volumes)
Bruce
On Fri, 6 Jan 2006, Goldman, Aaron (NIH/NIMH) [F]
wrote:
Hi, I downloaded the new version of mris_convert, but I'm having trouble
getting it to run successfully. When I start with bfloats it says
He wants to convert to the ascii surface format, so he needs
mris_convert (which will read all our "volume" formats).
Bruce Fischl wrote:
use mri_convert, not mris_convert (the version with the "s" is for
surfaces, not volumes)
Bruce
On Fri, 6 Jan 2006, Goldman, Aaron (NIH/NIMH) [F] wrote:
it will? Who knew? If they are just your "volume-encoded surface files",
then mri_convert should do the job, no?
On Fri, 6 Jan 2006, Doug Greve wrote:
He wants to convert to the ascii surface format, so he needs mris_convert
(which will read all our "volume" formats).
Bruce Fischl wrote:
mri_convert won't produce ascii surface format, will it?
Bruce Fischl wrote:
it will? Who knew? If they are just your "volume-encoded surface
files", then mri_convert should do the job, no?
On Fri, 6 Jan 2006, Doug Greve wrote:
He wants to convert to the ascii surface format, so he needs
no.
On Fri, 6 Jan 2006, Doug Greve wrote:
mri_convert won't produce ascii surface format, will it?
Bruce Fischl wrote:
it will? Who knew? If they are just your "volume-encoded surface files",
then mri_convert should do the job, no?
On Fri, 6 Jan 2006, Doug Greve wrote:
He wants to conv
I'm not sure how to explain this one, so I'll just include the output:
[whatever:mystudy] (nmr-std-env) stxgrinder-sess -analysis color01
-contrast color_bw_01 -sf sessid -df sesspar
--
stxgrinder-sess logfile is
/autofs/space/ship_006/us
Can you run paint-sess with the -debug option and send us the output?
On Fri, Jan 06, 2006 at 03:36:50PM +, Jane Aspell wrote:
> hi again
>
> we've been trying various things to get mk-fieldsign to work: installing the
> development version of freesurfer and trying it on a different compute
The command line is:
mris_glm --design $df --surfmeas thickness
--hemi $h --trgsubj $ts --nsmooth 300 --beta beta.mgh --var var.mgh
And each column of the design file is:
subject_name 1
And then, when I try to run mris_convert
-c beta.mgh beta.asc, it just gives me the usa
Hi,
We were running free-surfer (freesurfer-Linux-rh9-dev20051003-full.tar.gz)
on RedHat 9 and encountered a problem with the command mri_mask. It is not
at all working.
Here is what we entered as input:
mri_mask input.mgz mask.mgz output.mgz
No matter what we put as the mask, the input.mgz
what is in the mask.mgz volume?
On Fri, 6 Jan 2006, Yuhong Jiang wrote:
Hi,
We were running free-surfer (freesurfer-Linux-rh9-dev20051003-full.tar.gz) on
RedHat 9 and encountered a problem with the command mri_mask. It is not at
all working.
Here is what we entered as input:
mri_mask input
Hello everybody,
Does anybody have any experience with Scientific Linux? How
does it compare with
Fedora Core in terms of computational performance?
Will I still be able to use Red Hat FreeSurfer release on a
PC running Scientific Linux?
Thank you.
Regards,
Renat.
Renat,
We do not use Scientific Linux here at MGH, but we do use Centos4, which
is an Enterprise Linux variant. We use release 4.2, for both the 32bit
and 64bit platforms, so our Centos4 Freesurfer releases should be
compatible with Scientific Linux. (Also, Centos4 is based on
kernel-2.6.9, as i
Hi Bruce,
The exact input is:
mri_mask T1.mgz brain.mgz brain.mgz
This command was invoked by "recon-all -subjid subject
-normalization2", which is part of "recon-all -subjid subject
-autorecon2". Because of the bug, after this command, the manual
edited brain.mgz went back to pre-manual editin
Hi all,
I posted a message earlier today from the end of my rope and I think it
was a bit terse. Apologies.
I'm hoping that someone might have some insight into a (different) problem
that's come up with inorm.
I'm analyzing three identical subjects. The first two went through fine,
but the thir
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