Hi,
I didn't generated the surface myself (a technician in my lab did), but I
imagine it entailed the same process as for a subject, just using the MNI152
brain instead of a single individual's anatomical image. I'm hoping to find
the location on this surface of several peak coordinates from pas
Hi Ben,
I'm still confused. How do you get a surface from an MNI average? Or is
it from the colin dataset? Can you tell us a bit more about what you are
trying to do so we can see if we can help?
cheers,
Bruce
On Tue, 8 Sep 2009
benjamin.d...@yale.edu wrote:
>
> Hi,
>
> The surface isn't from
Hi,
The surface isn't from an individual subject, but generated from MNI space
itself. What exactly do you mean by sample it onto the surface? I could make
an image file with value one at the coordinate of interest and zero elsewhere,
and then overlay it on surface space and see where it lies,
Hi all,
When I use tkmedit and tksurfer to view the volume or surface, the image
display window just fleets once. I click the tag and it doesn't show up
either.
What's more, the menus of tkmedit don't response when I click them,
besides the menu of "Edit".
I just use the test command
Hi Ben,
any given MNI coordinate may or may not be on the surface of a subject.
You can convert it to individual subject space then sample it onto the
surface.
cheers,
Bruce
On Tue, 8 Sep 2009 benjamin.d...@yale.edu wrote:
>
> Hi,
>
> I'm wondering how to convert a single voxel coordinate in 2
Hi,
I'm wondering how to convert a single voxel coordinate in 2mm MNI152 space to a
location on a cortical surface representation of MNI space generated by
Freesurfer. My broader goal is to present a set of coordinates collected for a
meta-analysis on surface space. Thanks,
Ben Deen
Department
Hi, Bruce.
Thanks for your reply - it appears that this has happened before (though I'm
not exactly certain how often) and we suspect it could happen again in the
future. You mentioned editing the aseg.mgz - would you point us to the place
on the Wiki page that details how this is done and als
yes, you are *not* drawing the boundary. You are setting control points
inside the wm in regions in which the white matter signal intensity in
the normalized image (e.g. brain.mgz) is too low, meaning significantly
lower than 110
On Tue, 8 Sep 2009, Nick Schmansky wrote:
> Ritobrato,
>
> The us
Ritobrato,
The user doesnt have explicit control over where the surface boundaries
are drawn. Rather, you just have to be very careful not to put a
control point in grey matter, or any thing partial-volumed. I can't
quite tell from the resolution of the image you posted, but it appears
some of t
Thx Nick for the reply.
Then how do I make sure that the spline (that I have used control points to
demarcate) is included in the white matter boundary ?
Ri
- Original Message -
From: "Nick Schmansky"
To: "Bruce Fischl"
Cc: "Ritobrato Datta" , "freesurfer"
Sent: Tuesday, September
Ritobrato,
The control points mark voxels as belonging to white matter, and should
be marked sparingly. They are not points on a spline, as it appears you
were trying to do in the image.
Nick
On Tue, 2009-09-08 at 13:39 -0400, Bruce Fischl wrote:
> Hi Ri,
>
> you have to be careful to only put
Philipp,
Those warnings can be ignored.
Nick
On Tue, 2009-09-08 at 11:07 +0200, Philipp Klein wrote:
> Hello,
>
> I installed version 4.50 of freesurfer on a Ubuntu 8.10 system, the tests
> listed in the wiki all run well. Starting tksurfer with other data a
> warning is shown in the terminal
How much memory does your system have? Someone recently had this same
repeatable problem, and after they upgraded their system from 2GB to
4GB, the problem disappeared. We now recommend systems have at least
4GB of memory.
Also, it helps to include the recon-all.log file for the subject, to
help
Hi Ri,
you have to be careful to only put the control points in voxels that are
completely white matter (no partial voluming). I also don't know what you
mean by "the control points didnt get converted to a continuous line". Can
you elaborate?
cheers,
Bruce
On
Tue, 8 Sep 2009, Ritobrato Datta
A 2-3 year post-doctoral position is available at the Human Neuroscience
Laboratory of The University of Chicago (www.humanneuroscience.org). The
ideal candidate should be interested in the study of the neural basis of
language and/or neural plasticity characterized by changes in brain
networks
This seems to be a very new problem, associated with recent OSs. Some
googling of the error message:
Error: cannot restore segment prot after reloc: Permission denied
turns-up these results:
http://www.appistry.com/community/forums/content/cannot-restore-segment-prot-after-reloc-permission-deni
Hi Guang,
the volumes should be comparable to the unconformed ones.
cheers,
Bruce
On
Tue, 8 Sep 2009, Guang Zeng wrote:
>
> Hi, there,
>
> I converted a subject from nii (160x256x256) to mgz (256 x 256 x 256 ), and
> then sent it to
> the FreeSurfer pipeline.
>
> Now, I'd like to compare the r
Hi, there,
I converted a subject from nii (160x256x256) to mgz (256 x 256 x 256 ), and
then sent it to
the FreeSurfer pipeline.
Now, I'd like to compare the resulted hippocampus volume with a hand tracing
hippocampus using the original volume.
What is the best way to do it? I think I can not
hmmm, we haven't seen any of these in a while. Can you send us the
transforms/talairach.m3z and the recon-all.log file? And maybe the
transforms/talairach.lta and the norm.mgz
Bruce
On Tue, 8 Sep 2009, QQ Liu wrote:
> Hi all,
>When I run the FreeSurfer with one scan images(128) of a subjec
Hello,
I have managed to get FS installed onto my Centos virtual machine and I'm
currently trying to carry out the testing of my installation. I got to the qdec
part and got the following:
[...@localhost freesurfer]$ qdec
qdec.bin: error while loading shared libraries:
/usr/local/freesurfer/li
Hi all,
When I run the FreeSurfer with one scan images(128) of a subject, I am
getting the error message as follows:
Segmentation fault
ERROR: mri_ca_register with non-zero status 139
but continuing despite the error
#--
#...@# CA Reg Inv Fri Sep 4 23:59:5
Hello,
I installed version 4.50 of freesurfer on a Ubuntu 8.10 system, the tests
listed in the wiki all run well. Starting tksurfer with other data a
warning is shown in the terminal (the talairach.xfm can't be found), but
the program starts after that. As far as we can judge after a quick
examin
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