Hi,
Our lab have managed to generate ROIs in T1 images using Freesurfer, which
led to .label files. We succesfully measured the cortical thickness in
these ROIs for each subject in Freesurfer. Now we are aiming to track white
matter fibers from these ROIs in a tractography software Trackvis. Howev
Dear Marie,
Thank you, I use bash and changed my .bashrc and this worked, I previously
had used wrong syntax. Thank you very much for your help. However, I now
recieve another error and do not know what it means at all. I copy in the
error ! Thank you.
Improper assignment with rectangular empty m
Hi
Would you please let me know if it is possible to calculate the power
for a group comparison in cortical thickness? Also, a referee is
requesting F-values and T map , are they generated by q-dec?
That would be great if I can get an answer in more detail since I have seen
the post in FAQ, just
Hi Tommi,
> I am preparing to CVS register 30+ subjects to improve FSL probabilistic
> tractography alignment across subjects. First, thanks for a really cool
> tool! Then, I have some questions:
>
> 1. mri_cvs_register step1 is spherical registration. However, I have
> already run FS5.3 recon-a
Hi Zeke,
that did the trick!!
Thanks so much for your help!
sven
On 24-okt-2013, at 21:40, Z K wrote:
> Sven,
>
> Well that certainly is odd that. My guess is that there is some sort of
> extension that Mac is hiding in the finder window (along the lines of what
> you were talking about w
Rujing,
mri_strp_skull is not a FreeSurfer binary.
-Zeke
On 10/28/2013 01:31 AM, Rujing Zha wrote:
> Dear FreeSurfer Users,
> I downloaded FreeSurfer latest version in this
> website:ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.v
Hello Natalie,
'nu_correct' should be found in your '$FREESURFER_HOME/mni/bin'
directory. That directory should be added to your PATH when your source
the SetUpFreeSurfer.sh file. You can probably get around this issue by
adding $FREESURFER_HOME/mni/bin to your PATH environment variable. But
I
Thanks Lilla!
Which MNI152 version was used as template when doing nonlinear
CVS-registering from cvs_avg35 into MNI152 space? For example, was this
MNI152 ICBM 2009a 1mm Nonlinear Asymmetric?
Bests, Tommi
>
> Hi Tommi,
>
>
>> I am preparing to CVS register 30+ subjects to improve FSL probabili
Hi all,
I recently updated to FreeSurfer version 5.3.0, and I am now having
problems with freeview that I didn't have on the older versions. When I go
to "Surfaces" and "Load Labels", it only shows one label at a time.
Previously, I could add several labels and all would appear on the Figure.
Doe
Hi, I haven't received any word so re-sending in the event my email was
missed.
I am wondering what might be causing the volume stat issue-- is there a
problem with permissions in a file or something else entirely?
Thanks for any input,
Best,
Erin
--
Erin Walsh, Ph.D.
Postdoctoral Research As
Hi Lindsay,
I think there was no such option to display multiple surface labels at
once even in the old version. However, we will add it in the future.
Best,
Ruopeng
On 10/28/2013 01:48 PM, Lindsay Squeglia wrote:
Hi all,
I recently updated to FreeSurfer version 5.3.0, and I am now having
Hi Zeke,
Thanks so much for your prompt response. My PATH variable
is /usr/global/freesurfer/5.3.0/freesurfer. I do see nu_correct in
the /usr/global/freesurfer/5.3.0/freesurfer/mni/bin, so that seems to be
correct as well.
Should I export my PATH environment variable to include /mni/bin?
Thank
Hi Linn,
We have an issue using lGI with matlab 2013 in the current version. It will be
updated in the new version, but in the mean time if you want to use it, it's a
very small change that you have to do. See the following post:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg305
Was that from freeview or tksurfer?
On 10/28/2013 02:06 PM, Lindsay Squeglia wrote:
Hi Ruopeng,
Thanks for your response! I used to do it all the time in the previous
versions of FreeSurfer (see attached). I am not sure why the new
version is different.
Thanks!
Lindsay
On Mon, Oct 28, 2
Hi all,
I would like to calculate the 95% confidence interval of the slope for a
thickness cluster (vs age in years) produced by mri_glmfit-sim.
I have obtained values for my clusters from gamma.mgh and gammavar.mgh using
these two commands:
mri_segstats --i gamma.mgh
--seg m
It was definitely from freeview. These are the notes I wrote for creating
figures previously, and I didn't have a problem:
**Type freeview in command line in file where Freesurfer fsaverage brain
is, will open file, go to File--> Load Surface -->fsaverage-->surf. Choose
lh.pial; then do again for
Hi Anastasia,
I've attached my configuration file, and below is pasted the contents of
the error log. Below that, I've pasted the last few lines of the trac-all
log (not the error log), because it says something about a "dyld" that
cannot be loaded...might be related to the problem.
Thanks,
Mike
Mike,
You need to install XQuartz:
http://xquartz.macosforge.org/landing/
Also see the following troubleshooting page:
http://ftp.nmr.mgh.harvard.edu/fswiki/freesurfer_GUIs_troubleshooting
-Zeke
On 10/28/2013 03:17 PM, Michael Datko wrote:
> Hi Anastasia,
> I've attached my configuration file,
The XQuartz website you linked makes it sound like it is identical to X11,
is it different in some way? I have X11 already and it works flawlessly
with other applications such as AFNI and FSL.
On Mon, Oct 28, 2013 at 12:36 PM, Z K wrote:
> Mike,
>
> You need to install XQuartz:
> http://xquart
Hello,
I installed XQuartz and the processing gets a little bit farther than it
did before. However, I now run into an error about not being able to move
the bvecs file. To my knowledge I specified the bvecs file correctly (in
the same log file I attached previously), and it is in a format that h
Im of the understanding that X11 and XQuartz will not conflict. Many
users running Mac OSX Snow Leopard have both applications installed on
their systems. But if you are extremely weary of potential issues than I
suppose you could create a symbolic link from /opt/X11 to /usr/X11.
Additional sym
Hi Michael - Two things: First, in the dmrirc that you attached
previously, the bvecfile and bvalfile lines are commented out. Second,
these files need to be in column, not row format, as shown in the
tutorial:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula
Hope this helps,
a.y
Hi Jon
The segmentation looks really poor, which probably causes a topological defect
resulting in what you see. I would try using expert opts to set the
segmentation thresholds better
Cheers
Bruce
> On Oct 28, 2013, at 1:10 PM, Jonathan Holt wrote:
>
> FS experts,
>
> both of these surfaces
Where can I find more info on expert opts?
> On Oct 28, 2013, at 6:22 PM, Bruce Fischl wrote:
>
> Hi Jon
> The segmentation looks really poor, which probably causes a topological
> defect resulting in what you see. I would try using expert opts to set the
> segmentation thresholds better
> Che
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