Re: [Freesurfer] Using tksurfer to dispaly the surface

2009-09-22 Thread Nick Schmansky
QQ, Does the sample subject 'bert', found in freesurfer/subjects/bert, display overlays correctly? ie. does thickness display normally? I need to disambiguate whether its a system problem or a data problem. If bert doesnt display correctly, then I'd try updating the graphics driver. Also, are

[Freesurfer] Getting Started

2009-09-22 Thread Weisinger, Brian (NIH/OD) [E]
I must be really cpu challenged because I can't even seem to get this thing started. I am trying to perform basic set up right now. I have downloaded freesurfer so far and in the freesurfer setup and configuration section of the wiki I have been able to If using bash or sh, type: export

Re: [Freesurfer] Getting Started

2009-09-22 Thread Pedro Paulo de Magalhães Oliveira Junior
Try this: cd ~ vi .bashrc You wont see the .bashrc unless you use ls -a --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom --- Novo Netfilter 3.2 www.Netfilter.com.br --- Novo Netfilter Small Business

[Freesurfer] Bvecs and image orientation

2009-09-22 Thread Satrajit Ghosh
This question was asked on the FSL list and I thought it would be pertinent on this list as well in relation to mri_convert. -- Forwarded message -- From: Saad Jbabdi s...@fmrib.ox.ac.uk The bvecs are supposed to be relative to the image grid. On 22 Sep 2009, at 13:34, Laura

[Freesurfer] How do Control Points and Pial Surfaces Interact?

2009-09-22 Thread Sherri Novis
Hello - I am trying to compare normalized segmentation stats across groups. We are adding control points to the white matter in an attempt to push out the pial surfaces when it appears grey matter has been clipped or cut short.I am loading the following: tkmedit [SubjectID]

Re: [Freesurfer] Using tksurfer to dispaly the surface

2009-09-22 Thread QQ Liu
Hi Nick, It cannot display correctly for bert either. I have asked the question of displaying in tksurfer and tkmedit. I cannot fix the image window such as fsaverage. And I have to input the command exit in terminal to colse the window of fsaverage. I cannot close it by right-click the

[Freesurfer] FSL to FreeSurfer registration

2009-09-22 Thread Estephan Moana
Hello all, I took the FS course last June at the OHBM in San Francisco, and am now playing with it to get to know it better. One of the slides on the talk about FSL-FS integration mentioned that the input data (from FEAT) for the reg-feat2anat command should have not been smoothed prior to