Dear Douglas
Thanks for your reply. unfortunatey I still get the same error. Here is the
terminal output. Is there anything else I can do?
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/frees
Hi all,
I'm trying to get gyrification information about a single subject. I've
run the -localGI process but I have a few questions about the results:
1. When I try to plot the smoothed out pial surface over the brainmask in
freeview, I use the command
freeview -v subject/mri/brainmask.mgz -f s
Hi Bruce,
I performed both cp and wm edits and was able to fix most of the subjects in
the meantime. I’ll still see if I can get it ftp’d over to you guys to take a
look for future reference.
thanks!
Adam
Hi Adam
it's impossible to say without seeing some examples. If you upload a
proble
Thanks a lot for your input, I’ll give it a try.
Roberta
On 27 Oct 2014, at 17:58, Ruopeng Wang
mailto:rpw...@nmr.mgh.harvard.edu>> wrote:
Hi Roberta, not sure how well you know freeview. You can set the opacity of
overlay either from 'Configure Overlay' button on the GUI or from the
command-
Hi Christian,
Yes, you can use the ICV from the cross-sectional processing as
co-variate. The longitudinal stream assumes head-size is not changing
much in a few steps, but is still relatively robust in capturing large
brain changes. I have never tested it thoroughly in kids and am not sure
wh
Hi Roberta, not sure how well you know freeview. You can set the opacity
of overlay either from 'Configure Overlay' button on the GUI or from the
command-line by ':opacity=0.5'.
Ruopeng
On 10/27/2014 12:53 PM, Bruce Fischl wrote:
Hi Roberta
you are probably better off doing this in freeview
Hi Roberta
you are probably better off doing this in freeview - Ruopeng can help you
there.
cheers
Bruce
On Mon, 27 Oct 2014, Roberta Santoro wrote:
Dear all,
I have selected some vertices that I would like to overlay on an inflated surface
and I would like the overlay to have opacity<1 su
Make sure to use "piecewise" or "linear" thresholding and not "linear
opaque"
doug
On 10/27/2014 12:49 PM, Roberta Santoro wrote:
> Dear all,
>
> I have selected some vertices that I would like to overlay on an inflated
> surface and I would like the overlay to have opacity<1 such that I can see
Dear all,
I have selected some vertices that I would like to overlay on an inflated
surface and I would like the overlay to have opacity<1 such that I can see the
curvature underneath. I am using a script for doing this and everything works,
but the opacity doesn’t change when I use the command
Hi Kirstie
there is no easy answer to this question, but there are some guidelines:
1. The size of the smoothing kernel depends on the size of the effect you
are looking for and how well you expect it to align across subjects. For
example, you would need a far smaller smoothing kernel if you ex
Hi everyone,
Firstly - thank you for the excellent tools. This year has been my first
foray into surfaced based analysis and I'm enjoying it very much.
I don't currently have a gut instinct for an appropriate level of surface
smoothing. I'm sure that can't be easily answered but would a range of,
We don't have tools to do this. Not sure who does, but I think there are
some out there.
doug
On 10/27/2014 11:23 AM, Linda Douw wrote:
> Dear freesurfers,
>
> I have a bit of a strange question: does anyone know a way to write a
> template T1 brain (for instance fsaverage or MNI152) to dicom fil
Dear freesurfers,
I have a bit of a strange question: does anyone know a way to write a
template T1 brain (for instance fsaverage or MNI152) to dicom files? I
have some very old software that only takes dicoms and it's the only
software I can use to replicate previous findings, but obviously going
All CSF measures are ventricular, not sulcal. If you are in doubt, you
can always load the aseg.mgz and see what labels correspond to what. You
can also see
http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats
doug
On 10/27/14 9:40 AM, Mahmoud wrote:
Dear Doug,
The problem is that I'
Dear Doug,
The problem is that I'm not sure what those terms exactly mean ! i.e. what
is exactly CSF ? ventricles contain CSF right ? Is CSF counts for subdural
CSF too ? I have a the aseg.stats with all terms inside but not sure which
one to pick up, that's why I'm asked here.
Thank you,
Mahmoud
You probably want something like BrainSegNotVent/Sum(CSF and Ventricles)
Is that what you mean?
doug
On 10/26/14 11:45 PM, Mahmoud wrote:
Dear all,
I used the the 3 steps of longitudinal analysis explained in
freesurfer longitudinal tutorial and need to compute the ratio
Parenchyma/CSF for
Hello Freesurfer Community,
I am now having issues getting qdec to launch as well. The qdec window pops
up momentarily but then disappears. This is the error message I get:
error: xp_attach_gl_context returned: 2
X Error of failed request: 0
Major opcode of failed request: 149 (GLX)
Minor
Dear Martin and FS experts,
I have a small follow-up question regarding the post below. Given a young
sample where ICV is still growing, that I want to control for this and that the
data look ok: Can I use the cross-sectional ICV as a covariate in analyses on
the longitudinal data? Or will this
Dear FreeSurfer experts,
I am searching for a publication highlighting a better accuracy of FreeSurfer compared to SPM with regard to the analysis of cortical gray matter volumes. Does anybody know one?
Thanks for your help!
Best, Marisa
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