On Mon, Mar 9, 2009 at 3:02 PM, Douglas N Greve <
greve@nmr.mgh.harvard.edu <mailto:
greve@nmr.mgh.harvard.edu>> wrote:
I think I've found the problem in that the original annotation at
a vertex is not being cleared if a cluster is not there.
The short term fix is to delete " --annot aparc" from
mri_glmfit-sim at line 353. I'll email when I have a longer term
fix. What platform are you using?
doug
Devdutta W wrote:
When I load mc-z.abs.2.sig.cluster.mgh, if the "Draw filled
labels" button is toggled on, it looks no different from
before. Toggling the "show overlay" button doesn't do anything.
If the "Draw Outlined labels" button is toggled on, the
outlines of the colored regions can be seen (including the
outlines of the clusters). This time, toggling the overlay
button on-off shows the clusters.
On Mon, Mar 9, 2009 at 2:12 PM, Douglas N Greve
<
greve@nmr.mgh.harvard.edu <mailto:
greve@nmr.mgh.harvard.edu>
<mailto:
greve@nmr.mgh.harvard.edu
<mailto:
greve@nmr.mgh.harvard.edu>>> wrote:
/what does it look like when you load
mc-z.abs.2.sig.cluster.mgh
as an overlay?/
Devdutta W wrote:
Nick, Sita,
The average subject is created from our data, perhaps
that's
why it looks different. We were having problems getting
freesurfer to recognize our average subject. So we linked
fsaverage to our average subject. I didn't see a
button (or a
tool) to toggle on-off the annotation. The overlay
button is
there but toggling it doesn't do anything.
There indeed are clusters mixed in with the
annotations. But
from the documenation, it seems that the command we are
using
is /supposed/ to show clusters (but only the clusters,
not the
the annotations). And that is the question I am trying
to get
answered.
Here is the command we are using:
/tksurfer fsaverage lh inflated -annot
mc-z.abs.2.sig.ocn.annot -fthresh 2 -curv -gray/
I am running this command from the appropriate folder and
fsaverage is linked to our average subject. We are
using the
following documentation:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis?highlight=(mri
<
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis?highlight=%28mri>
<
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis?highlight=%28mri>
<
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis?highlight=%28mri>\_glmfit\-sim)
Thanks,
Devdutta
On Mon, Mar 9, 2009 at 12:09 PM, Nick Schmansky
<
nicks@nmr.mgh.harvard.edu
<mailto:
nicks@nmr.mgh.harvard.edu>
<mailto:
nicks@nmr.mgh.harvard.edu
<mailto:
nicks@nmr.mgh.harvard.edu>>
<mailto:
nicks@nmr.mgh.harvard.edu
<mailto:
nicks@nmr.mgh.harvard.edu>
<mailto:
nicks@nmr.mgh.harvard.edu
<mailto:
nicks@nmr.mgh.harvard.edu>>>> wrote:
Devdutta,
What version of freesurfer is being used? The fsaverage
subject you
show doesnt look right. Also, I see what appear to
be clusters
mixed in
with the annotations. The summary files output by
the multiple
correction step will tell you how many and the size
of the
clusters.
You should be able to toggle on-off both the
annotation and the
overlay
independently.
I am cc'ing Sita, as she may be able to help you on
this (I
will have
limited email contact this week).
Nick
On Mon, 2009-03-09 at 11:21 -0500, Devdutta W wrote:
> Forgot to attach the images, again.
>
>
> On Mon, Mar 9, 2009 at 11:20 AM, Devdutta W
<
devdutta.w@gmail.com <mailto:
devdutta.w@gmail.com>
<mailto:
devdutta.w@gmail.com <mailto:
devdutta.w@gmail.com>>
<mailto:
devdutta.w@gmail.com
<mailto:
devdutta.w@gmail.com> <mailto:
devdutta.w@gmail.com
<mailto:
devdutta.w@gmail.com>>>>
> wrote:
> Hi Nick,
> Can you shed some light on why this might be
happening? I
> will attach the two picture again in case
you weren't
able to
> view them last time. I tried what I
thought you
meant by
> "turn off annotation display" and I have
stated what
happened
> in my previous email (please see below)
>
> * If I don't include the -annot
option in
tksurfer it
> only displays the fsaverage,
naturally.
> * If I toggle off the button that
says "show
labels", it
> looks like it is just the
fsaverage as well.
> * If I toggle on the "Draw outlined
labels"
button it
> shows the same regions as before
except
they are
> merely outlined, not filled.
> Any help you can give me will be appreciated.
>
> Thanks,
> Devdutta
>
>
> On Wed, Mar 4, 2009 at 10:36 AM, Devdutta W
> <
devdutta.w@gmail.com
<mailto:
devdutta.w@gmail.com>
<mailto:
devdutta.w@gmail.com