[Freesurfer] Freesurfer installation on RHEL 5.4: failed to create OpenGL rendering context

under the Windows host), and did not run into such a problem Can you help me figure out why it's running into this problem and how to fix it? Thanks! Dahlia. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu

[Freesurfer] sliver problem remains after going through relevant wiki page

anyone instruct me how to resolve this issue? Thanks!! Dahlia. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] sliver problem remains after going through relevant wiki page

unappealing. Can anyone instruct me how to resolve this issue? Thanks!! Dahlia. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] centOS vs. ubuntu

these two packages will work under ubuntu, and what other advantages/disadvantages I should expect. Thanks for any advice!!! Dahlia. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] VMware?

For running Freesurfer and MNE on Linux, is there any reason not to use VMware Workstation instead of having a dual boot machine? Thanks!! Dahlia. Hi, Will Freesurfer and MNE work on CentOS 5 (I see in the Download page that CentOS 4 is supported, but I understand that most workstations

[Freesurfer] VMware?

For running Freesurfer and MNE on Linux, is there any reason not to use VMware Workstation instead of having a dual boot machine? Thanks!! Dahlia. Hi, Will Freesurfer and MNE work on CentOS 5 (I see in the Download page that CentOS 4 is supported, but I understand that most workstations

[Freesurfer] mkbrainmask not finding fslmaths

Hi, I ran the following preproc-sess command and mkbrainmask-sess failed, with an error message of not finding fsmaths. I don't know where to be looking for this file and what previous command should have generated it. Can anyone help me out? Thanks! Dahlia. I ran: preproc-sess -sf

[Freesurfer] Re: mkbrainmask not finding fslmaths

it. Can anyone help me out? Thanks! Dahlia. I ran: preproc-sess -sf sessid_subj31.txt -df sesspar -fwhm 5 The error message was: ERROR: cannot find either fslmaths for avwmaths ERROR: mkbrainmask failed ERROR: mkbrainmask-sess failed mkbrainmask-sess.log says: mkbrainmask-sess $Id

Re: [Freesurfer] Freesurfer installation: tksurfer not drawing

an error message surfer: ### redraw failed: no gl window open The installation is over Fedora Core 6 (build x86_64) How do I correct this? Thanks! Dahlia. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] Freesurfer installation: tksurfer not drawing

I correct this? Thanks! Dahlia. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer

[Freesurfer] white.surf doesn't follow wm.mgz

Hi, What should I do when the white volume looks right (e.g. filled in where needed) but the white surface doesn't follow the boundary of the volume? I've done recon-all with autorecon2-wm and autorecon3. Thanks! Dahlia. ___ Freesurfer mailing list

[Freesurfer] dicom image viewer

Hi, What do people usually use to view dicom images, and how do I invoke this viewer? Thanks! Dahlia. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

RE: [Freesurfer] mri_annotation2label

I was using the std version. It works well under dev. Thanks! Dahlia. By the way, the FSwiki entry on mri_annotation2label does not mention the annotation command option (but perhaps this is on purpose?) From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Monday, October 30

[Freesurfer] tables for mri_annotation2label

Hi, When running mri_annotation2label, what is the correct table to give the --table option for ?h.aparc.annot ? $FREESURFER_HOME/Simple_surface_labels2005.txt is the table for ?h.aparc.a2005s.annot, right? Thanks! Dahlia. ___ Freesurfer mailing

[Freesurfer] tables for mri_annotation2label (fwd)

In the same vein of mri_annotation2label: When I ran mri_annotation2label --subject subj25_bay2 --hemi rh --labelbase $SUBJECTS_DIR/subj25_bay2/label/aparc-rh --table $FREESURFER_HOME/Simple_surface_labels2005.txt (where $SUBJECTS_DIR is ~dahlia/structurals/) on mirabai in the nmr-std-env

Re: [Freesurfer] visualizing surfaces

Hi Camilo, You can load a 3rd surface by going to: File Aux Surface Load Aux Surface Configuration Pial Vertices and then choosing whatever surface you want (doesn't have to be pial, can be a BEM). Dahlia. On Fri, 25 Aug 2006 [EMAIL PROTECTED] wrote: Hi Freesurfer, Is there a way

Re: [Freesurfer] visualizing surfaces

for BEMs it'll work... On Fri, 25 Aug 2006, Bruce Fischl wrote: only if they have the same # of faces/vertices though. Scuba is much more general. On Fri, 25 Aug 2006, Dahlia Sharon wrote: Hi Camilo, You can load a 3rd surface by going to: File Aux Surface Load Aux Surface Configuration

RE: [Freesurfer] BEMs

use just the mprage for mri_watershed. Best, Dahlia. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Saturday, August 19, 2006 6:45 PM To: [EMAIL PROTECTED]; freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] BEMs Hi, I am doing

[Freesurfer] retinotopy starting with blanks

Hi, I'm analyzing a retinotopy data-set in which each scan started with 2 TRs of a blank screen, and then proceeded to 8 cycles as usual. Is there any possibility to tell a retinotopy analysis to ignore these 2 TRs? Thanks! Dahlia. PS - I can't answer as to why these 2 blank TRs were put

[Freesurfer] segmentation fault for: mris_convert

Hi, I'm trying to use mris_convert and am getting a segmentation fault error. The precise steps are pasted below. Can anyone figure out why this is happening now? Thanks! Dahlia. mirabai:dahlia[81] setenv SUBJECTS_DIR ~/structurals/ mirabai:dahlia[82] nmrenv freesurfer-Linux

[Freesurfer] tksurfer: left arrow in dev version

Hi, When working under nmr-dev-env, tksurfer gives me the following error message when I press the left arrow button (and doesn't move the surface): Error: can't read 'extTransform(translate,dist)': no such variable. Am I doing something wrong? Thanks! Dahlia

[Freesurfer] saving open lines

Hi, Is there a way to save an open line drawn on a subject's surface to load on the surface in a future tksurfer use? Thanks, Dahlia. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo

[Freesurfer] recalculating surfaces

this without guidance so as not to make mistakes and start stepping over other files. Can you tell me which commands to run to regenerate these surfaces correctly? Thanks!!! Dahlia. PS - the subject is ~dahlia/structurals/subj21_bay2 ___ Freesurfer mailing list

Re: [Freesurfer] recalculating surfaces

rerun stage2 and then stages 34, will that recalculate the correct surfaces from the (currently correct) mri/wm? Thanks! Dahlia. On Thu, 27 Oct 2005, Evelina Busa wrote: Hi Dahlia Since it seems unclear whether or not you edited the WM volume of this second subject whose surface files were

Re: [Freesurfer] recalculating surfaces

the mri/wm/ volume is still correct, will I now get the correct old surfaces? Thanks! Dahlia. On Thu, 27 Oct 2005, Evelina Busa wrote: Hi again, Yes, assuming you are using the same version of FreeSurfer and since the WM volume is the same, the new surfaces you created should be similar