hmm, not sure what happened on the 2nd run, but you should be able to
corect those problems by putting some control points in superior regions
(in the white matter at the base of the strands that are lost). Make sure
they are completely in the wm and not in partial-volumed voxels.
Bruce
On T
Hi,
Does anyone know if it is possible to generate an aparc.stats file for an
average subject? mris_anatomical stats does not seem like it will work
because it requires wm.mgz which is not generated in the
make_average_subject process. I would like to find the number of vertices
and the surface ar
Cameron,
mris_info
will show number of vertices and surface area, and other basic stats,
for a surface file.
Nick
On Thu, 2007-10-25 at 11:06 -0400, Cameron Ellis wrote:
> Hi,
> Does anyone know if it is possible to generate an aparc.stats file for an
> average subject? mris_anatomical stats
Actually, I think it still needs the --tfmt because it cannot determine
that it is a curv file from the name of the file.
doug
Nick Schmansky wrote:
Support for the curv format as a target was added to mri_surf2surf in
freesurfer v4.0. For your version, you can just exclude the -tfmt curv
pa
Xin,
It sounds like you will need to get the newer mri_surf2surf to create
the thickness difference maps you want. You can either install the
v4.0.1 of freesurfer, or I have posted just mri_surf2surf for you to
copy to your existing install. That file is located here:
ftp://surfer.nmr.mgh.harva
Hello,
Thought that this might be of interest:
We've found a case for which the talairach.xfm is grossly wrong (checked
using tkregister2) but the automatic-failure detection of version 4.0.1
indicated no problems.
#
[EMAIL PROTECTED] Talairach Failure
Mike,
Can you send me the input files for that subject? That is, the files
found in this directory of yours:
/disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/010502_61774/mri/orig
If so, you can upload them to me via the filedrop:
https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
N
Dear All,
We are dealing with MPRAGE data acquired at a 3.0T MRI scanner and
analyzed with FS 3.0.5.
Images belong to a group of Multiple Sclerosis patients.
We would like to ask some questions and we apologize for the fact that
we have quite a number of them :-)
First, regarding measure
On Thu, 25 Oct 2007, Gallo, Antonio (NIH/NINDS) [F] wrote:
Dear All,
We are dealing with MPRAGE data acquired at a 3.0T MRI scanner and
analyzed with FS 3.0.5.
Images belong to a group of Multiple Sclerosis patients.
We would like to ask some questions and we apologize for the fact that
we
Hi all,
I've been having problems with make_average_subject. The command and error
are below. Below this is the same command with the output generated by the
--debug flag.
I am running version 4.0 (redhat) on Linux Debian.
I'd appreciate any help on this.
Thanks,
Alex
make_average_surface --su
Alex,
It looks like the subject 'testavg' already exists. To overwrite it,
add --force to the make_average_subject, or choose a different name for
the --out arg (or delete the 'testavg' subject).
Nick
On Fri, 2007-10-26 at 11:03 +1000, Alexander Fornito wrote:
> Hi all,
> I've been having prob
Sorry, I ran the --debug flag after running the first command. It is not
the cause of the error. Here is the output after testavg has been deleted.
make_average_surface --subjects cann01 cann02 cann04 cann05 cann06 cann07
cann08 cann09 cann10 cann13 cann14 cann15 cann16 cann17 cann18 cann19
cann2
Alex,
The make_average_ scripts are such that they will exit on any
error encountered (via the -e arg to tcsh at the top of the script).
It appears make_average_surface is exiting after executing the command:
id | tee -
a
/data/kang/work/struct/alex/freesurfer/subjects_cann/testavg/scripts/make
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