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 <gr...@nmr.mgh.harvard.edu>wrote: > > 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 < >> gr...@nmr.mgh.harvard.edu <mailto:gr...@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 >> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@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 >> > >> < >> 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> >> <mailto:ni...@nmr.mgh.harvard.edu >> <mailto:ni...@nmr.mgh.harvard.edu>> >> <mailto:ni...@nmr.mgh.harvard.edu >> <mailto:ni...@nmr.mgh.harvard.edu> >> <mailto: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> >> <mailto:devdutt...@gmail.com <mailto:devdutt...@gmail.com>> >> <mailto:devdutt...@gmail.com >> <mailto:devdutt...@gmail.com> <mailto: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> >> <mailto:devdutt...@gmail.com >> <mailto:devdutt...@gmail.com>> <mailto:devdutt...@gmail.com >> <mailto:devdutt...@gmail.com> >> >> <mailto: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> >> <mailto:ni...@nmr.mgh.harvard.edu >> <mailto:ni...@nmr.mgh.harvard.edu>> >> <mailto:ni...@nmr.mgh.harvard.edu >> <mailto:ni...@nmr.mgh.harvard.edu> >> <mailto: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> >> <mailto:devdutt...@gmail.com <mailto:devdutt...@gmail.com>> >> <mailto:devdutt...@gmail.com >> <mailto:devdutt...@gmail.com> <mailto: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 >> > > >> > >> > > >> > >> _______________________________________________ >> > > 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 >> >> >> >>
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