On Mon, Mar 9, 2009 at 3:02 PM, Douglas N Greve <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>> 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>\_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>>> 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>>>

> 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

<mailto:devdutta.w@gmail.com>>> wrote:
> Nick,
> I confess, I am not exactly sure what you
mean by
> "turn off annotation display". I tried a few
> things.
>
> * 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.
> These were the only ones that I could
think of. Is
> that what you meant or was it something
else that I
> missed?
>
> Thanks,
> Devdutta
>
>
> On Tue, Mar 3, 2009 at 7:12 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>>> wrote:
> What is displayed if you turn off the
> annotation display?
>
> The threshold in the simulation
is used to
> determine whether clusters
> are found or not. A threshold of 2
indicates
> a p-value of 0.01
> (1/(10^2), 3 is 0.001, etc. The
threshold
> referred to in the tksurfer
> display is just for color
thresholding.
>
> Nick
>
>
> On Tue, 2009-03-03 at 17:17 -0600,
Devdutta W
> wrote:
> > Forgot the attachments earlier.
Here they
> are now
> >
> > On Tue, Mar 3, 2009 at 5:11 PM,
Devdutta W
> <devdutta.w@gmail.com
<mailto:devdutta.w@gmail.com>
<mailto:devdutta.w@gmail.com <mailto:devdutta.w@gmail.com>>>

> > wrote:
> > Hi Freesurfers,
> > More questions about this
analysis.
> > 1) Referring to the
documentation,
> we used the following
> > command:
> > tksurfer fsaverage lh
inflated -
> annot mc-
> > z.abs.2.sig.ocn.annot
-fthresh 2 -
> curv -gray
> >
> > The documentation says we
should see
> an image as shown in
> > Figure 1 (attached).
But what we
> see is Figure 2 (also
> > attached). Can
somebody explain
> this?
> >
> > 2) When running the
simulation
does
> it matter what threshold
> > we use? For example,
can we use a
> threshold of 2 or 3
> > (instead of 4 as shown in
> documentation) when running
> > mri_glmfit-sim? And do
we have to
> use the same threshold
> > while displaying the
clusters
after?
> >
> > Thanks for any help.
> >
> > Devdutta
> >
>
> >
> _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
<mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>

> >
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>
>
>

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