/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>\_glmfit\-sim)
Thanks,
Devdutta
On Mon, Mar 9, 2009 at 12:09 PM, Nick Schmansky
<ni...@nmr.mgh.harvard.edu <mailto:ni...@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
<devdutt...@gmail.com <mailto:devdutt...@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
> <devdutt...@gmail.com <mailto:devdutt...@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
> <ni...@nmr.mgh.harvard.edu
<mailto:ni...@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
> <devdutt...@gmail.com
<mailto:devdutt...@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
> >
>
> >
>
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> >
>
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>
>
>
>
>
>
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