That's hard as I'll just be guessing. What is the intensity of the wm just
inside the white surface where you are missing pial? And why can't you send an
image?
Cheers
Bruce
On Feb 21, 2013, at 11:11 AM, melinaki p-t wrote:
> I am afraid I can't...
> Can you give any advise without pictures?
Usually what I do is create a sym link called "current" that I point to
the newest version of Freesurfer. e.g.
cd /usr/local/freesurfer
ln -s $PWD/freesurfer-5.1.0 current
So then in my .bashrc file I set
FREESURFER_HOME='/usr/local/freesurfer/current'
Obviously you can change this if you wante
I don't think either one of these are errors, just warnings that occur
pretty frequently and I don't think should impact the results. Does the
recon finish? Do the results look ok?
On Fri, 22 Feb 2013, Blessy M wrote:
I am getting the bottom two sets of errors while doing a simple recon-all.
Hello,
I manually checked the registration of my free surfer parcellations to the
rsfMRI data after reg-feat2anat and aseg2feat.
Problem is that I had to scale (stretch) the functional to make a good fit in
several cases. Is this recommended? How can I avoid this?
Thanks,
S
___
Hello Kalli,
In the past this issue has been related to out-of-date NVIDIA drivers. If
you open a terminal and type 'glxgears' do you see a window pop-up
with 3 colored gears running? If not, email the help desk and ask them to
update your NVIDIA drivers.
-Zeke
> Hi all,
> I am a new student at
Hi all,
I am a new student at the Martinos and very new to the freesurfer community - I
am actually in the learning process for the moment.
Today after passing the tkmedit command I keep getting the following message:
"GLUT: Fatal error in tkmedit.bin: visual with necessary capabilities not
fou
I am getting the bottom two sets of errors while doing a simple recon-all.
More specifically while running this command:
recon-all -subjid . -noskullstrip -autorecon1 -notal-check -autorecon2
-autorecon3
Has someone encountered this kind of errors? Is there a fix?
1)
Computing MAP estimate using
cc'ing the freesurfer list so other with the same issue may reference.
Original Message
Subject: Re: [Freesurfer] tkregister2 window error: Remote login
From:"Sudhin A. Shah"
Date:Fri, February 22, 2013 10:51 am
To: "zkauf...
Sulc is the integrated dot product of the surface normal and the movement
vectors during inflation
Bruce
On Feb 22, 2013, at 12:25 PM, Martin Reuter wrote:
> Hi Andrew,
>
> I don't know how the sulc measure gets computed and what it means exactly.
> Probably someone else can tell.
>
> The
Hi Catherine
Is not ideal. Ou could copy your subjects and try rerunning with dev (keeping
edits)
Bruce
On Feb 22, 2013, at 12:14 PM, Rongxiang Tang wrote:
> Hi Bruce,
>>
>> Just want to follow up on the error issue:
>>
>> It seems that using the stable version for two of the subjects will
Hi Andrew,
I don't know how the sulc measure gets computed and what it means
exactly. Probably someone else can tell.
The longitudinal treatment is identical as for example thickness. The
slope (rate) is a fit into the data across time. So a negative slope
means a reduction in whatever is me
Hi Bruce,
>
> Just want to follow up on the error issue:
>
> It seems that using the stable version for two of the subjects will always
> give incomplete surface outputand if using the dev version, it seems to
> require updating the entire binaries to avoid the error.
>
> I was thinking th
hm, I just realized that I should probably run selxavg3-sess with
-svres and then take the residuals from the res folder, right?
caspar
2013/2/22 Caspar M. Schwiedrzik :
> Dear Freesurfer experts,
> I am running some functional connectivity analyses using FSFAST in
> Freesurfer 5.1.
> I would like
Dear Freesurfer experts,
I am running some functional connectivity analyses using FSFAST in
Freesurfer 5.1.
I would like to compare seed time courses (which I later use as
predictors) obtained after regular pre-processing with seed time
courses obtained after regressing out several nuisance paramet
Hello Sudhin,
>From what I can tell, it appears that is it possible you have a
compatibility issue between Exceed OpenGL and Mesa GLX (and thus not
directly a freesurfer issue).
It turns out if your system's libGL.so library is provided by Mesa
7.1 or later, OpenGL applications will not run remot
Hello
I have run free surfer and co-registered with the rsfMRI via FSL (reg-feat2anat
& aseg2feat)
When I extract the values (as per the matlab code below), I see NaNs in certain
regions. Of the 19 datasets that I have analyzed I have see NaNs for the
following labels
10061033
On Feb 21, 2013, at 2:16 PM, Sudhin A. Shah wrote:
> Hello,
>
> I am remotely logged in to my Ubuntu system(from Mac). I have previously run
> tkregister2 but am now having trouble;
>
> Opening window subj
> Window type not found
> register: tkoinitwindow(name) failed.
>
> Is there a solution
Dear Freesurfers,
I came across a possible issue during the automatic labeling of V1 using
the Hinds method
(http://surfer.nmr.mgh.harvard.edu/fswiki/BrodmannAreaMaps). If you use
the command "recon-all -s subjid -label_v1", as far as I can see, mainly
the shell script "predict_v1.sh" in $FRE
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