[Freesurfer] adjust pial surface outward for abnormally thick cortex

2015-04-17 Thread Jonathan DuBois
Hi Freesurfers, I am having trouble manually correcting the surface of brain with an abnorally thick cortex due to a malformation. It seems as though there is a thickness threshold that constrains the pial surface reconstruction. I have added control points to the white matter but the problem seem

Re: [Freesurfer] Is the linux centos package compiled with openmp enabled?

2015-04-17 Thread Z K
It is compiled with the "-fopenmp" flag. -Zeke On 04/16/2015 09:01 PM, jupiter wrote: > Hi, > > I've installed FreeSurfer from a binary package > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz., does that > package was compiled witn ---enable-openmp? > > Thank you. > > Kind regards, > >

Re: [Freesurfer] Advice - best method, longitudinal vs. cross-sectional

2015-04-17 Thread Bruce Fischl
you should also plot them on the same axes (or at the very least with the same limits) On Fri, 17 Apr 2015, Martin Reuter wrote: Hi Pradeep, is this the result of a single subject? In a single subject lot's of things can happen (e.g. motion artefacts can affect a single time point, other imagi

Re: [Freesurfer] Advice - best method, longitudinal vs. cross-sectional

2015-04-17 Thread Martin Reuter
Hi Pradeep, is this the result of a single subject? In a single subject lot's of things can happen (e.g. motion artefacts can affect a single time point, other imaging or measurement noise will have effects). Also how far are the time points apart? Run the same thing with 20 subjects and you

Re: [Freesurfer] Content of register.dof6.dat.param

2015-04-17 Thread pfannmoelj
Hello Doug, just a very last question. Where ist the origin of the coordinate system if the motion parameters are calculated using mc-afni2 and where is it if BBR is used? I mean the origin in the coordinate system of the input and output volume. Yours pfannmoe On Mon, 13 Apr 2015 10:36:02 -0