Can you run make_average_surface and make_average_volume separately?
Brian Schweinsburg, Ph.D. wrote:
I ran it with make_average_subject --debug \
--subjects SC010 SC012 ...
I also tried it with --echo. It provides no output.
I checked the script and it is executable. I looked through
Title: Re: [Freesurfer] make_average_subject error?
Hi Doug,
The same thing happens when I try to run them separately. It exits to the prompt with no messages.
Brian
--
Brian C. Schweinsburg, Ph.D.
Assistant Adjunct Professor of Psychiatry
University of California, San Diego
Office:
Hi, I am trying to install and set-up freesurfer on a SuSE Linux system, I
downloaded and installed the Redhat version, I'm not sure if this was the
correct version to use, but when I try to fix the perl path with the command
given on the wiki, it says that the command is not found, nor is
Jeff,
Can you tell me the error it is saying about MINC?
Also, do you have a prior installation of the MINC tools? I am guessing
you do, and that there is some prior setting of the MINC_BIN_DIR and
MINC_LIB_DIR variables that is conflicting with the new installation.
The MINC toolkit is
Try editing those scripts so that the first line is:
#!/bin/tcsh -efxv
ie, adding "xv"
This turns on all kinds of debugging
Brian Schweinsburg, Ph.D. wrote:
Re: [Freesurfer] make_average_subject error?
Hi
Doug,
The same thing happens when I try to run them separately. It exits to
Hi,
I'm using version freesurfer-Linux-centos4.0_x86_64-dev20050921-full.
After recon-all ... -autorecon1, the skull is stripped but a decent
portion of the meninges remain. I tried using
recon-all -skullstrip -wsthresh h -subjid ID
I ran that with h=20, h=10 and h=2. It didn't seem to help so
Hi Michele,
it may not matter. Typically we don't use the cortical aseg, but the
surface-based on instead.
Bruce
On Tue, 27 Sep 2005, Michele Perry wrote:
Hi,
I'm using version freesurfer-Linux-centos4.0_x86_64-dev20050921-full.
After recon-all ... -autorecon1, the skull is stripped but a
On Sep 27, 2005, at 3:06 PM, [EMAIL PROTECTED] wrote:Message: 2Date: Tue, 27 Sep 2005 13:42:02 -0400From: Keith Schneider [EMAIL PROTECTED]Subject: [Freesurfer] mri_convert doesn't recognize DICOM filesTo: freesurfer@nmr.mgh.harvard.eduMessage-ID: [EMAIL PROTECTED]Content-Type: text/plain;
Blaise (and Keith),
I was able to recreate the problem that Keith is seeing using a sample
dicom file he sent, so I am working to resolve that issue. It seems to
be a Mac-centric issue, as the same dicom will convert correctly on
Linux.
The odd thing is that the siemens_dicom files output from
Hi,
I'm trying to create an annotation file from a volume is mris_sample_parc.
Is there any way to have it resample at 0.5 the distance between the white
and pial surfaces?
Thanks
Satra
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Hi Satra,
that's what it does by default.
cheers,
Bruce
On Tue, 27 Sep 2005, Satrajit Ghosh wrote:
Hi,
I'm trying to create an annotation file from a volume is mris_sample_parc.
Is there any way to have it resample at 0.5 the distance between the white
and pial surfaces?
Thanks
Satra
Hi,
I've been having some problems with some of my images where the pial surface
misses some parts of some gyri. Just wandering what the best way to fix this
is. I've experimented changing the intensities using the configure volume brush
tool in tkmedit with some success, but was wandering if
Hi Alex,
it depends what the cause is. I think the most common is either bias
field or intrinsic tissue variations. These can be fixed if the white
matter at the base of the strand isn't intensity normalized, that is, if it
has a value 110 in the T1 image. If that's the case, you can add some
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