Re: [Freesurfer] maybe a problem of tcl

2006-12-21 Thread Nick Schmansky
lv bin, The Ubuntu Linux variant is not one I have experience with, so there may be issues there. Maybe others on the list can comment on their experiences with Ubuntu. tksurfer (and tkmedit and tkregister2) have wrapper scripts which declare paths and LD_LIBRARY_PATH settings pointing to the Tc

Re: [Freesurfer] maybe a problem of tcl

2006-12-21 Thread lv bin
Nick, Thanks for your reply! My Linux OS is Ubuntu 6.06 (AMD 64),I want to ask you if the tksurfer refers to "tclsh/tclsh8.4",and which "tclsh8.4"? I have tried the fllowing command,and hope these to help you know the problem more clearly. %locate tclsh8.4 /usr/bin/tclsh8.4 /usr/local/fre

[Freesurfer] GLM - Multiple Comparisons

2006-12-21 Thread David Zai
In running a glm analysis with multiple classes (A, B, C, D, E, F) and no variables, is it better to: (1) have one fsgd with a contrast vector of (1 -1 0 0 0 0) to compare Group A thickness to Group B thickness, or (2) should I make an fsgd with just my Group A and B subjects and have my contrast

RE: [Freesurfer] variability

2006-12-21 Thread Nick Schmansky
Valentina, The randomization in the algorithms accounts for about a 0.02% change in thickness results. You can disable randomness (or rather, force seeding the rng with same number) by including the flag -norandomness with recon-all. This flag is available in v3.0.4. In older versions, do this

Re: [Freesurfer] maybe a problem of tcl

2006-12-21 Thread Nick Schmansky
Iv, Which Linux OS is this installed upon? I know there have been some problems with freeglut, but thought they were resolved. Nick On Wed, 2006-12-20 at 16:45 +0800, lv bin wrote: > hi, > > I am a newcomer of freesurfer.Sereral days ago,I installed the > freesurfer(its version is freesurfer-

[Freesurfer] unpacksdcmdir & multiple volume protocols

2006-12-21 Thread Sebastian Moeller
Hi Doug, hi List, I ran into slight problems with unpacksdcmdir. I acquired some combined proton density and T2 volumes with one sequence (plus a bunch of additional slices from Inline/generic tab on out allegra menue), which resulted in mri_convert choling at the import of the second part of

RE: [Freesurfer] variability

2006-12-21 Thread Durastanti, Valentina (NIH/NINDS) [F]
Could you please quantify "almost"? could you also please explain me how can I eventually disable the randomization? I have another question that I've already put on the list but the answer never came, maybe is not clear enough: I have two classes (patients and healthy volunteers) and one variable