Re: [Freesurfer] set up of initial data directories

2008-07-30 Thread Bruce Fischl
HI Stephen, not quite raw image space, but mostly. Definitely not tal coords. We resample into a 256^3 volume aligned with the native scanner coords. cheers, Bruce On Wed, 30 Jul 2008, Stephen Rose wrote: Hi I am a new freesurfer user so I apologize in advance for the basic questions.

Re: [Freesurfer] set up of initial data directories

2008-07-30 Thread Jenni Pacheco
Hi Stephen, To follow up, your command line should work just fine, and will set up the directories you need. Jenni On Wed, Jul 30, 2008 at 6:56 AM, Bruce Fischl [EMAIL PROTECTED]wrote: HI Stephen, not quite raw image space, but mostly. Definitely not tal coords. We resample into a 256^3

[Freesurfer] again: qdec error

2008-07-30 Thread Dorit Kliemann
Dear all, I wanted to open qdec for the first time and experienced an error that was posted some days ago... ( RE: [Freesurfer] qdec ERROR: Rendering vtkXOpenGLRenderWindow ; Juranek, Jenifer ) ERROR: In /usr/pubsw/packages/vtk/5.0.4/src/VTK/Rendering/vtkXOpenGLRenderWindow.cxx, line 219

Re: [Freesurfer] mri_watershed regions appearing round edge, freesurfer 4.0.2

2008-07-30 Thread Bruce Fischl
Hi Ian, mri_watershed minimizes a risk functional in which we weigh the cost of leaving non-brain voxels to be much less than stripping true brain ones, so it does sometimes leave stuff around. Is this causing any problems? Bruce On Wed, 30 Jul 2008, Ian Malone wrote: Hi, Has anyone