Re: [Freesurfer] Vertex number

a slight correction: surface vertices go from 0-> nverts-1 matrix(in matlab) will go from 1-> nverts Brian T. Quinn wrote: Hi Brian, I read in a surface file and it spit out 3 coordinates, do you know if they are RAS and also there is no vertex number with them, so does the vertex number st

RE: [Freesurfer] edit white matter lesion

Thanks for your answer. For the slice with white matter lesion, I need to manually fill the ventricle. Am I right? Do I need to fill the ventricle in the slices that I don't edit anything at all? Thanks, Antao > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] Beh

Re: [Freesurfer] Vertex number

Sarah: Freesurfer surface file formats are documented at: http://grahamwideman.com/gw/brain/fs/surfacefileformats.htm ... including the "W" file format (scroll down). The coordinate system for FreeSurfer's vertices is RAS, described in more detail at: http://grahamwideman.com/gw/brain/fs/coor

Re: [Freesurfer] Vertex number

Hi Brian, I read in a surface file and it spit out 3 coordinates, do you know if they are RAS and also there is no vertex number with them, so does the vertex number start at zero and count up then? they are RAS coords. surface vertices go from 0-> nverts matrix(in matlab) will go from 1-> nve

[Freesurfer] Going from Boston to Waltham?

Hi Is anyone going to Waltham from Boston or Charlestown for the FSL course? We're attending the course and would be very interested to join others for either a car ride from Boston (we don't have a car) or sharing a taxi from the Waltham station to the Doubletree Hotel. Alternatively, if anyone k

Re: [Freesurfer] Vertex number

Hi Brian, I read in a surface file and it spit out 3 coordinates, do you know if they are RAS and also there is no vertex number with them, so does the vertex number start at zero and count up then? One more quick question. Do I have to read in the hemisphere's separately or is there a surfac

Re: [Freesurfer] edit white matter lesion

Hi Antao, the ventricle isn't autofilled (yet). We're hoping to release a new version with this and other functionality in it sometime in the next month. cheers, Bruce On Fri, 15 Jul 2005, Antao Du wrote: Hi, I am trying to edit the white matter lesion in wm volume. when I open tkmedit sub

[Freesurfer] edit white matter lesion

Hi, I am trying to edit the white matter lesion in wm volume. when I open tkmedit subjid wm. There is a white matter lesion that was misclassified. I paint that region with white matter lesion to white color using button 2. Do I need to paint all ventricle? The manual says that the ventricle is au

Re: [Freesurfer] Vertex number

hi Sarah- you can you the matlab code in $FREESURFER/matlab to do this. use read_surf.m for this. -- brian On Fri, 15 Jul 2005, Sarah Rugheimer wrote: Hello, Does anybody know if there is a file with or a way to obtain a mapping of the vertex number with say the RAS coordinate system. I k

[Freesurfer] recon-all issue

First, I am a newcomer to the FreeSurfer community so bear with me. I have installed a snapshot of FreeSurfer for OSX: freesurfer-Darwin- tiger-full.dmg I seem to have everything working fine in terms of environment settings etc. I created a subject directory and populated it with some T1

[Freesurfer] Vertex number

Hello, Does anybody know if there is a file with or a way to obtain a mapping of the vertex number with say the RAS coordinate system. I know when you are in the tksurfer window by using the mouse/cursor you can see each vertex number with the corresponding RAS coordinate, but is there a way