[Freesurfer] surface format

Hi, Could you let me know the format of the surface generated by freesurfer? Is that easy to convert it to *.vtk? And also is the surface in the original subject space or in Talairach space? Thanks Anqi Qiu Center for Imaging Science The Johns Hopkins University

Re: [Freesurfer] having problem in running recon-all...

Shahab, libgsl is included with the freesurfer distribution, and a path is setup to point to it when the freesurfer setup script is 'sourced'. What is displayed when you type: source $FREESURFER_HOME/SetUpFreeSurfer.csh GSL_DIR should be one of the lines. Switching to suse should not be a pr

Re: [Freesurfer] surface format

Anqi, The default surface file generated by freesurfer is a proprietary format, but the freesurfer utility 'mris_convert' will convert to ascii and vtk formats (among others). Two examples: mris_convert rh.pial rh.pial.asc creates an ascii file of triangle vertices and faces, and: mris_con

Re: [Freesurfer] surface format

Hi Anqi, the surface is a binary format. You can convert it to ascii using mris_convert (the ascii format is defined on our wiki). They are in native space, not talairach. cheers, Bruce On Mon, 7 Aug 2006, Anqi Qiu wrote: Hi, Could you let me know the format of the surface generated by

[Freesurfer] Slackware 10.0.0

Hello all, I have a small query.Just wanted to know which stable Freesurfer version I should install for Linux Slackware 10.0.0 version. Has anybody experienced any issues usig this platform. Thanks in advance. Chacko Cherian. Arizona State University. _

[Freesurfer] Skull Stripping

Hello, After having run -autorecon1 on all of my subjects I've noticed skullstripping has edited out the cerebellum/brainstem on some, but not on others. Because I'm not interested in these structures, can I just leave the files as is (i.e.-not bother adjusting the wsthreshold level, re-running,

Re: [Freesurfer] Skull Stripping

Hi Derin, the subcortical segmentation will fail unless you correct it, as the registration will try and align a model with a cerebellum to a brain without one. sorry. Bruce On Mon, 7 Aug 2006, Derin Cobia wrote: Hello, After having run -autorecon1 on all of my subjects I've noticed skull

[Freesurfer] Recon all finished with errors, How do I see what errors?

I was running autorecon2-cp and it said it finished with errors, below are the recon-all.log and recon-all-status.log, I couldn't figure out what the error is. Mon Aug 7 10:37:16 PDT 2006 [EMAIL PROTECTED] Intensity Normalization2 Mon Aug 7 10:37:16 PDT 2006 [EMAIL PROTECTED] Mask BFS Mon Aug

Re: [Freesurfer] Recon all finished with errors, How do I see what errors?

Hi Jake, Did it write out the wm.seg.mgz file (would be in the subjects mri directory)? Is it possible that you either don't have write permissions in that directory or that you are out of disk space? Jenni On Mon, 7 Aug 2006, Jake Freimer wrote: I was running autorecon2-cp and it said it

Re: [Freesurfer] Slackware 10.0.0

Chacko, For Slackware 10, you should probably use the rh9 build of freesurfer, as rh9 uses the v2.4 kernel, as does Slackware 10. Nick On Mon, 2006-08-07 at 11:10 -0700, Chacko Cherian wrote: > Hello all, > > I have a small query.Just wanted to know which stable > Freesurfer version I should i

Re: [Freesurfer] Freesurfer install error OS Tiger, GSL error

On the Mac, libgsl is included with Freesurfer in the directory /Applications/freesurfer/lib/gsl. Can you confirm that your LD_LIBRARY_PATH and DYLD_LIBRARY_PATH environment variables contain those paths? That is, examine the output of: env | grep LD_LIBRARY Also, make sure that these vars do

[Freesurfer] TKMEdit error on Mac OS 10.4.7

Hi, I have a brand new Macbook pro with the dual-core intel chip. I downloaded and installed the most recent verision of freesurfer. When I run the configuration script I get source $FREESURFER_HOME/SetUpFreeSurfer.csh freesurfer-Darwin-tiger-stable-pub-v3.0.3 Setting up envi