Re: [Freesurfer] small volume correction

2010-05-10 Thread lordowen
Dear Prof. Greve: Thanks for your reply. But how can we constrain the search area in QDEC? Could you advise us more? We can manually create a ROI (and save it as a label) following the instruction of tutorial, but the FDR function in QDEC still corrected for whole brain but not the label area only

[Freesurfer] Bad pial surface - continued

2010-05-10 Thread Ed Gronenschild
Hi, I've mailed this once before and tried to solve a persistent problem. Reviewing the results of recon-all I noticed that the derived pial surface chopped away an unacceptable amount of gm voxels. First of all I tried to manually edit some wm voxels, however with no success. Then I tried another

[Freesurfer] tksurfer/tkmedit tcl scripting "could not open display" error

2010-05-10 Thread holmes
All, I have generated a batch script that saves out images from tkmedit and tksurfer which I would like to run on a cluster of workstations across a large dataset. However, when I run the jobs remotely tkmedit/tksurfer opens displays on my local machine. As a consequence, if I do not remain logged

Re: [Freesurfer] Bad pial surface - continued

2010-05-10 Thread Allison Stevens
Ed, do you want to send me the subject and I'll take a look? -- On Mon, 10 May 2010, Ed Gronenschild wrote: > Hi, > > I've mailed this once before and tried to solve a persistent problem. > Reviewing the results of recon-all I noticed that the derived pial > surface chopped away an unacceptable

Re: [Freesurfer] Talairach failure

2010-05-10 Thread Antoine Leflon
With tkregister2 I've just noticed my problem was that the movable is not done properly because when I switch on it I see a white screen or something blurred . any one could help ? Antoine leflon Bruce Fischl a

Re: [Freesurfer] Talairach failure

2010-05-10 Thread Bruce Fischl
can you get to the data before it got converted to analyze? If not, how will you ever know left from right? On Mon, 10 May 2010, Antoine Leflon wrote: With tkregister2 I've just noticed my problem was that the movable is not done properly because when I switch on it I see a white screen or som

[Freesurfer] Contrast Problem

2010-05-10 Thread Andrés Camarena
I am having an issue where the sig.nii file created after running mkanalysis and slxavg sets the value in a high contrast region to zero. Any idea what could be the problem. I've attached an image of the problem. -- Department of Aeronautics and Astronautics Massachusetts Institute of Technology

Re: [Freesurfer] Bad pial surface - continued

2010-05-10 Thread Bruce Fischl
Hi Ed, we can't help until we can accurately diagnose why it's happening. Have you checked for incorrectly fixed topological defects? cheers Bruce On Mon, 10 May 2010, Ed Gronenschild wrote: > Hi, > > I've mailed this once before and tried to solve a persistent problem. > Reviewing the result