Hi Joshua
If you look at our neuron paper:
https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl02-labeling.pdf
I think it's the Kennedy, 1989 reference
Cheers
Bruce
> On Jun 12, 2014, at 12:04 AM, Joshua Lee wrote:
>
> Dear Freesurfer Experts,
>
> I am trying to better understand what reg
I'm plotting potential distributions on a cortical surface using TkSurfer.
The color scale "Heat" gives the most comprehensible plots. However, I
would like to have the maximum values to be plotted in red instead of
yellow, and minimum in dark blue instead of light blue.
max+threshold0
Hi Matt
1. What template do you mean? We have multiple ones. The only MNI one we
have is for the linear talairach registration, which we barely use at
all.
2. How are you doing the editing? Is it in freeview or tkmedit? When we
edit the wm.mgz we track it by setting erased voxels to 1 (not 0
Hello Freesurfer experts,
I have two separate questions.
1. I am doing an MRI study on young children (3-5 years old). I have read in a
few a different places that Freesurfer isn't ideal for analyzing young
subjects. It does seem to be processing my subjects just fine though, with the
exceptio
Hi,
On a remote server forwarding X and running Ubuntu 14.04 I am having
difficulty running tkregister2, with this error:
*No glx extension!*
*register: ### tkoInitWindow(name) failed*
Also tried
*export LIBGL_ALWAYS_INDIRECT=y*
which did not work. Any input is highly appreciated.
Hi Doug,
The second command below should copy your edits from the finalsurf manedit in
cross to the long directory. You can try that command manually with a fresh
volume. If it really does not carry over, can you send me the two volumes
(edited one from cross and the unedited one from long) so t
Hi Anna, whenever it says qdec-long the table is in qdec format (with a
fsid-base as second column. It would then use the longitudinally processed
results, which is what you want , both for lme and 2 stage model.
Best Martin
Sent via my smartphone, please excuse brevity.
Original mess
Hi Tudor,
You'd add the lgi only to the third step (the -long runs). And you could do a
two stage model with it.
Martin
Sent via my smartphone, please excuse brevity.
Original message
From: Tudor Popescu
Date:06/10/2014 11:51 PM (GMT+01:00)
To: free surfer
Subject: [Free
Hi Anastasia,
Thanks for the reply.
After I edit my .tcshrc file to source the dev, I still get an error message.
glia:shantanu[64] mynmr53
MNE software location set to:/usr/pubsw/packages/mne/stable
MATLAB software not available
/usr/pubsw/packages/mne/stable/bin added to PATH
/usr/pubsw/
thanks.
On Fri, June 13, 2014 12:30 pm, Anastasia Yendiki wrote:
>
> The right one to source is /usr/local/freesurfer/nmr-dev-env
>
>
> On Fri, 13 Jun 2014, Shantanu Ghosh wrote:
>
>> Hi Anastasia,
>>
>> Thanks for the reply.
>>
>> After I edit my .tcshrc file to source the dev, I still get an err
The right one to source is /usr/local/freesurfer/nmr-dev-env
On Fri, 13 Jun 2014, Shantanu Ghosh wrote:
> Hi Anastasia,
>
> Thanks for the reply.
>
> After I edit my .tcshrc file to source the dev, I still get an error message.
>
> glia:shantanu[64] mynmr53
>
> MNE software location set to:
Hi Sal - There is no way to do this through trac-all, sorry.
a.y
On Fri, 6 Jun 2014, Salil Soman wrote:
> Hi,
> I noticed in the output for tracula -prep I am currently running using
> cvsreg it mentions openmp=1, I was wondering if there is a way to enable
> more than 1 core for openmp for tra
Hi Kathryn - The -stat option was added in the latest tracula update, see
here:
http://freesurfer.net/fswiki/Tracula/#Updates
You need to download this update, after installing freesurfer 5.3, to be
able to do what is described in the tutorials.
a.y
On Wed, 4 Jun 2014, Kathryn Cullen
Hi Shantanu - The -qa flag was added in the update to tracula that was
posted after the 5.3 release.
http://freesurfer.net/fswiki/Tracula/#Updates
Martinos Center users can simply switch to the dev version of freesurfer
to take advantage of these updates, in which case you don't need to
Hi Yoon - No, in the current code the assumption is that the b-values are
the same for all subjects in the study. One scenario where this wouldn't
be the case is if different DWI volumes are removed for different subjects
because of excessive motion, and we'll be able to handle this in the next
Hi Koen,
Thanks for such a prompt reply.
I visualized it in freeview with:
freeview nu.mgz -p-labels posterior_left_* posterior_Left-Hippocampus.mgz
-p-labels posterior_right* posterior_Right-Hippocampus.mgz -p-prefix
posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt
Thanks,
Joana
20
Hi Joana,
This looks like a visualization issue rather than a segmentation error to
me. How did you visualize this?
Koen
On Jun 13, 2014 2:59 PM, "Joana Braga Pereira"
wrote:
> Dear all,
>
> I'm running the GEMS tool in Freesurfer 5.3 to measure the volumes of
> hippocampal subfields in subjec
Hi dr Jerome J Maller
The analysis I do this research was followed as the tutorials of freesurfer
group analysis
(https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis). The
detailed was followed:
(1) recon-all autorecon-all; (2) recon-all -s
-localLGI; (3) recon-all -
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