Hi Doug, This is a follow up question regarding display issue from mri_glmfit-sim. The issue as you explained was that the original annotation was not being cleared. You suggested a short-term as well as a long-term fix.
The temporary fix was deleting "-annot aparc" from mri_glmfit-sim. As a more permanent fix, you emailed me a modified copy of mri_surfcluster. 1. My question is when re-running mri_glmfit-sim with the new mri_surfcluster do I still need to delete "-annot aparc" from mri_glmfit-sim? In other words, are both of these needed or will using the modified mri_surfcluster alone solve the problem? 2. Another question: Is there any way to convert the previous "bad" .annot file to "good" .annot file so we can view it without having to run mri_glmfit-sim again? We ran it with 5000 iterations and it took over 10 days. If there is a way we can get the same results without having to re-run it, I would very much like to know about it. Thank you for your help so far. Devdutta On Tue, Mar 17, 2009 at 12:26 PM, Devdutta W <devdutt...@gmail.com> wrote: > 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 >>> >>> >>> >>> >
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
