Hi,
I have run qdec for a simple contrast comparing thickness across the
cortical surface between a patient and control group. Not much
survives vertex-wise FDR correction, and I would like to try cluster-
based thresholding. I would like to make sure I understand the inputs
to the command.
Sarah,
Indeed you are correct! The rh9 freesurfer v4.0.1 distribution is
missing the fsl tools. I don't know how this happened, as the other
dists have it, but I have re-posted freesurfer-Linux-rh9-stable-pub-
v4.0.1.tar.gz, containing the fsl tools (actually, a subset of the full
fsl distributi
It should have been xdpyinfo, not xdpyino (note the 'f').
Sarah Andersen wrote:
Thank you.
When I run 'xdpyino | grep GL' it says "xdpyino: Command not found" (this is
in the tcsh shell)
I am running it on VMware Player version 2.0.2 and using the FSL_vm5_32
virtual machine from the FSL websi
Thank you.
When I run 'xdpyino | grep GL' it says "xdpyino: Command not found" (this is
in the tcsh shell)
I am running it on VMware Player version 2.0.2 and using the FSL_vm5_32
virtual machine from the FSL website. If this helps and you can give me
further instructions, I would greatly apprecia
i have installed version freesurfer-Linux-rh9-stable-pub-v4.0.1
and i do not see a dir for fsl, only fsafd and fsfast. i tend
to get the flirt error but this does not seem to affect the
completion of recon-all so i've ignored it 'til now. but just
wondering why i don't see an fsl directory if ther
Great! Thanks!
My subjects were ran in stable3, so they didn't have the BrainSegVolNotVent
measure in the aseg.stats. Rerunning segstats though..
Thanks again!
On Wed, 28 Nov 2007, Nick Schmansky wrote:
this wiki page has just been created to hold this info:
http://surfer.nmr.mgh.harvard.e
this wiki page has just been created to hold this info:
http://surfer.nmr.mgh.harvard.edu/fswiki/BrainVolume
On Wed, 2007-11-28 at 14:14 -0500, Doug Greve wrote:
> This is from mri_segstats --help
>
> MEASURES OF BRAIN VOLUME
>
> There will be four measures of brain volume in the output summar
This is from mri_segstats --help
MEASURES OF BRAIN VOLUME
There will be four measures of brain volume in the output summary file:
(1) BrainSegNotVent - sum of the volume of the structures identified in
the aseg.mgz volume this will include cerebellum but not ventricles,
CSF and dura.
Hi all,
I want to pull the measure of whole brain volume. In the aseg.stats there
is a BrainMaskVol and a BrainSegVol. Which one do I want?
As I understand it, BrainMaskVol is the volume of the brainmask (including
the ventricles) whereas BrainSegVol is the volume of brain matter and not
inclu
Your X server on your virtual Linux image does not appear to have GLX
support. If you run 'xdpyino | grep GL' do you see GLX listed?
If not, I am not sure what to say as I don't know what virtual machine
program you are using. But you need to read up in its docs about
how to properly install a
Dear FreeSurfers,
I am having a problem viewing in tksurfer: I can only see a sliver of the
brain. This sliver will rotate and do everything that tksurfer is supposed
to do, but I can't view any more of the brain than a tiny piece of the
occipital lobe. I have tried this with several different
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