Re: [Freesurfer] extracting BA6

2008-05-28 Thread Bruce Fischl
Hi Behrang, we have probabilistic labels for BA6, but it's a surface-based label. We haven't quite finished getting ready to distribute it, but hopefully in the next week or two. cheers Bruce On Wed, 28 May 2008, Behrang Nosrat Makouei wrote: Hi FreeSurfer Community, I was wondering if

[Freesurfer] extracting BA6

2008-05-28 Thread Behrang Nosrat Makouei
Hi FreeSurfer Community, I was wondering if we can extract BA6 from aseg.mgz or aparc+aseg.mgz I noticed BA6 was added after ver 4.0.3 but when I tried "mri_extract_label aparc+aseg.mgz 406 output.mgz" or "mri_extract_label aseg.mgz 406 output.mgz" I get empty volumes for the output.mgz. T

Re: [Freesurfer] sub-voxel projections

2008-05-28 Thread Doug Greve
I've put an x64 version here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2label If that does not match your OS, then let me know doug Ben Kennedy wrote: Thanks doug, can I have a newer version? My version (mri_label2lable --version) is stable4 and it doesn't

Re: [Freesurfer] sub-voxel projections

2008-05-28 Thread Ben Kennedy
Thanks doug, can I have a newer version? My version (mri_label2lable --version) is stable4 and it doesn't have a --paint option. Ben On May 28, 2008, at 11:39 AM, Doug Greve wrote: you can create a label with the coordinates, the use mri_label2label with the --paint option to sample them

Re: [Freesurfer] sub-voxel projections

2008-05-28 Thread Doug Greve
you can create a label with the coordinates, the use mri_label2label with the --paint option to sample them to the closest surface vertex. Two caveates: 1. You may need a new version of mri_label2label (I can get it to you if so) 2. You have to use the proper coordinates doug Ben Kennedy wrot

RE: [Freesurfer] tksurfer display broken: "smart" over-ride?

2008-05-28 Thread Paul Raines
Do you see any warnings (WW) or errors (EE) in your /var/log/Xorg.0.log file? What does running 'glxinfo' say? On Wed, 28 May 2008, Juranek, Jenifer wrote: Paul, Actually, I did follow your suggestion *first* to add the 3 lines to X11/xorg.conf (see tailed file below). However, after reboot

RE: [Freesurfer] tksurfer display broken: "smart" over-ride?

2008-05-28 Thread Juranek, Jenifer
Paul, Actually, I did follow your suggestion *first* to add the 3 lines to X11/xorg.conf (see tailed file below). However, after reboot, the same problem persisted. So I followed Krish's advice to look at a previous thread which referenced the mesa-libGL-*.rpm files @ MGH. My mistake for not k

Re: [Freesurfer] tksurfer display broken: "smart" over-ride?

2008-05-28 Thread Paul Raines
I don't understand why you got a mesa-libGL rpm and are trying to install it? I think doing so could really mess up your system so it is a good thing it is not letting you. My email was about adding Section "Extensions" Option "Composite" "Disable" EndSection to your /etc/X11/xorg.co

[Freesurfer] sub-voxel projections

2008-05-28 Thread Ben Kennedy
Dear Freesurfer, I've been playing around with Freesurfer and monkey MR volumes, and I'm trying to find some sort of foothold to use Freesurfer more effectively. I have the surfaces and inflated volumes of the brain, and I also have a bunch of sub-voxel coordinates (in the T1 volume) of

[Freesurfer] tksurfer display broken: "smart" over-ride?

2008-05-28 Thread Juranek, Jenifer
Krish & Paul, Many thanks for the quick advice. I have downloaded the mesa-libGL-6.5.1-7.2.el5.x86_64.rpm from the RH network to my desktop. However, a "smart" window pops up reporting that "a newer version than /home/jjuranek/Desktop/mesa-libGL-6.5.1-7.2.el5.x86_64.rpm is already installed". I