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... _glmfit-sim)
Thanks, Devdutta
On Mon, Mar 9, 2009 at 12:09 PM, Nick Schmansky nicks@nmr.mgh.harvard.eduwrote:
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 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> 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> 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> > 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 >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer