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
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.
- 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?
- 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
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
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.eduwrote:
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
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.eduwrote:
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
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
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
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
/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... 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> 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>> > 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>> 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>> 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>> > > 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> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.eduwrote:
/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...https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis?highlight=%28mri< 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.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>
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 whathappened
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 "showlabels", 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>> 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.edumailto: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 2indicates
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 thisanalysis.
> 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 weshould 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 simulationdoes
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 clustersafter?
> > Thanks for any help. > > Devdutta > >
> Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 > > > > > > ------------------------------------------------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
We are using Red Hat Enterprise Linux 5. Thanks for your help. I'll try that out.
On Mon, Mar 9, 2009 at 3:02 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
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...https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis?highlight=%28mri < https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis?highlight...
<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.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 > > > > > >
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Try copying this: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surfcluster
into your $FREESURFER_HOME/bin directory (make a backup first), and then re-run.
doug
Devdutta W wrote:
We are using Red Hat Enterprise Linux 5. Thanks for your help. I'll try that out.
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 <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: > 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>> <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: > 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>> <mailto: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>> <mailto: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 > > > > > > ------------------------------------------------------------------------ _______________________________________________ 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
Hi Doug, Thanks for your help. A followup question to your last email: the short term fix that you mentioned earlier, do I need to make that fix in addition to copying the new mri_surfcluster file in the binary dir? Or has that been fixed already?
Thanks, Devdutta
On Mon, Mar 9, 2009 at 4:41 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Try copying this:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_surfcluster
into your $FREESURFER_HOME/bin directory (make a backup first), and then re-run.
doug
Devdutta W wrote:
We are using Red Hat Enterprise Linux 5. Thanks for your help. I'll try that out.
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...https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis?highlight=%28mri < https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis?highlight...
<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis?highlight...
<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.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 <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: > 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>> <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: > 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>> <mailto: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> <mailto: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 > > > > > >
_______________________________________________ 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
Hi,
my follow up question would be, how much has changed regarding fsaverage between freesurfer version 4.1.0 and 4.3.1? Is the added insula label the only change that has been made? Besides, when I load both annotations, the old and the new one, it seems to me almost every border of the parcellation has been shifted slightly. Is it how it's meant to be? I ask because I forgot to update the fsaverage in my separately stored Subjects_dir since version 4.1.0 and made a lot of analysis in the last months. To my mind it's good enough to rerun mri_surfcluster with the new fsaverage to get the updated annotations into my summary tables. Should that do the trick?
Thanks again, Georg
---------------------------------------------------------------------------- -------
Iris, the registration targets were derived differently. With version 4, we automatically fill in all the ventricles. In verion 3, they were partially filled in manually. Version 3 creates a surface around the ventrical making it look like a sulcus, and this affects both the target and the registration to the target. So, on most of the surface, the registration will be very close, but it will deviate signifiacntly around the ventricles/medial wall. I think the fsfast in version 4 should work fine with the anatomicals (including fsaverage) of version 3.
doug
Steinmann, Iris wrote:
Hi,
we have several reconstructed brains, which were processed by freesurfer 3.0.5. We also kept using the fsaverage data from 3.0.5 in order to be consistent. We wish to do fMRI analysis with freesurfer/fs-fast 4.0.5 and found that talairach coordinates differ slightly when using the fsaverage from version 3.0.5 and the current fsaverage from 4.0.5. Yet, the both volumes appear pretty similar, the newer one maybe a little bit smoother. We would like to know what constitutes the exact difference between these two fsaverage datasets and whether it is possible to use the new version for analysis with the "old" fsaverage data without getting inconsistent results.
Thanks a lot, Iris _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Devdutta W -
Douglas N Greve -
Georg Homola -
Nick Schmansky