[Freesurfer] questions regarding freesurfer 4.0.5

2008-06-18 Thread Sebastian Moeller
First, if this shows up twice, let m apologise for mixing up my email addresses... Aloha fellow surfers, I just installed ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer-Darwin-leopard-i686-stable-pub-v4.0.5-full.dmg on my: intel macbook, running 10.5.3 with 4GB of RAM. A few observat

[Freesurfer] orientation problem when converting from SPM .nii format to bshort

2008-06-18 Thread Leila Reddy
Hi, I am trying to convert SPM5 .nii files into bshort and I used the following command: mri_concat fkoch-0007*.nii --o bold/007/fspm_000.bshort The command seems to work in that I have a bunch of bshort files in my bold/007 directory but when I try to view the slices (using sliceview-sess fo

[Freesurfer] Re: Further questions regarding freesurfer 4.0.5

2008-06-18 Thread Liat Levita
Hi all, we are also having some problems with v4.05 (Mac computer PC Tiger) -we keep getting problems with edit segmentation All seems well until we perform the following sequance of actions: 1. Press mouse button 3 to erase voxels from a particular ROI. 2. Press mouse button 2 to add voxels

Re: [Freesurfer] ICV accuracy

2008-06-18 Thread Jared Conley
Thanks, Bruce. That seemed to work well. Jared -- Jared Conley Center for Neurological Imaging Brigham and Women's Hospital Harvard Medical School 221 Longwood Ave., RF 394 P: 617.525.6238 Bruce Fischl wrote: Hi Jared, you can load the source (nu_noneck.mgz) and target (/autofs/space/

Re: [Freesurfer] questions regarding freesurfer 4.0.5

2008-06-18 Thread Nick Schmansky
Sebastian, responses: point 1) yes, sorry, no freeview yet for the mac. still trying to get the wxWidgets library (a relatively new one for us) to work on the mac with the freeview code. freeview is still very new though. point 2) we just recently got a 64bit mac (the old was was a mac mini, w

[Freesurfer] FreeSurfer tksurfer

2008-06-18 Thread Pedro Brito Cruz
Dear all, i'm a newbie using FreeSurfer and recently installed the CentOS 4 x86_64 version on my 64 bit processor with Linux Ubuntu (dapper version). I followed the tutorial for testing the installation and tkmedit tool worked fine but tksurfer did not. I got the following error, tksurfer bert

Re: [Freesurfer] FreeSurfer tksurfer

2008-06-18 Thread Pedro Paulo de Magalhães Oliveira Junior
Hi Pedro, If you are using NVidia I suggest you to check if you are using latest Ubuntu native Nvidia driver. Best Regards, Pedro Paulo Oliveira Jr. 2008/6/18 Pedro Brito Cruz <[EMAIL PROTECTED]>: > Dear all, > > i'm a newbie using FreeSurfer and recently installed the CentOS 4 x86_64 > version

[Freesurfer] 2D images

2008-06-18 Thread jewet037
Hi, I would like to create a properly proportioned 2-dimensional map of hemispheric surfaces to use for displaying average vertex values within parcellated regions or individual values for each vertex. At the moment, we can access the matrix of vertex values (i.e. the scalars computed at each vert

Re: [Freesurfer] 2D images

2008-06-18 Thread Bruce Fischl
Hi Ethan, the ?h.aparc.annot (or ?h.aparc.a205.annot) file contains the cortical region names, and you can cut and flatten individual hemisphere, or the fsaverage surface has pre-flattened cortical hemispheres you can use if you want. cheers, Bruce On Wed, 18 Jun 2008 [EMAIL PROTECTED] wr