Re: [Freesurfer] fsl + freesurfer

Gui, Have you had a look at the tutorial page that describes the FSL/Freesurfer integration? https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial see slide #4, and session 2b. I can't offer any other help than this, as I do not have experience performing this integration, but your approach is s

RE: [Freesurfer] mris_anatomical_stats

Antonio, There was a bug in mris_anatomical_state that was preventing the log file from being written. Which freesurfer OS dist do you use? I can post a fixed version of the binary. Nick On Tue, 2007-12-18 at 16:03 -0500, Gallo, Antonio (NIH/NINDS) [F] wrote: > Hi Nick, > This is what I wrote

[Freesurfer] fsl + freesurfer

Hi-I am trying to work out a work flow of integrating fsl and freesurfer. the basic goal is to do surface-based group analysis. what I have now is the run1.feat, run2.feat and mean.gfeat for each subject done by FSL Feat and the processing anatomy using recon-all in freesurfer. so the question now

Re: [Freesurfer] hole in pial surface

Hi Matt, I didn't get a screenshot, but if the Euler number is okay, you should be fine. Bruce On Tue, 18 Dec 2007, Matt Colvin wrote: Dear Freesurfer gurus: I have come across two brains which appear to have small holes in the pial surface when viewed in tkmedit. Each hole appeared for on

RE: [Freesurfer] mris_anatomical_stats

Hi Nick, This is what I wrote (FS 4.0.1): mris_anatomical_stats -log logfile -l ?h.cortex.label subjid ?h NB: the logfile is created but is empty. Thanks, Antonio >-Original Message- >From: Nick Schmansky [mailto:[EMAIL PROTECTED] >Sent: Tuesday, December 18, 2007 3:10 PM >To: Gallo,

[Freesurfer] hole in pial surface

Dear Freesurfer gurus: I have come across two brains which appear to have small holes in the pial surface when viewed in tkmedit. Each hole appeared for only one slice. Performing mris_euler_number on all the appropriate surfaces yielded no aberrant results (ie, =2, no defects). Further, there did

Re: [Freesurfer] mris_anatomical_stats

Antonio, Can you send me a command-line that shows usage of creation of the log file? That is, where it should be created, but isnt. In v3.0.5, the last three measures that you mention are wrong, and this problem was fixed in v4.0.0. Does the v4.0 mris_anatomical_stats always produce results fo

Re: [Freesurfer] qdec BadMatch error

Hi Lisa, I have found a solution for your problem: Before running Qdec, execute: export XLIB_SKIP_ARGB_VISUALS=1 It will fix this problem until Ubuntu and NVidia resolve the open issue with GLX. Best Regards, Pedro Paulo Jr

[Freesurfer] mris_anatomical_stats

Hi All, Could you please help with the following: When we run mris_anatomical_stats with FS 4.0.1 we can see the results on the terminal and we are able to get a log file, but this latter appears always blank. Countrarywise, when we use mris_anatomical_stats with FS 3.0.5 on the same set of d

Re: [Freesurfer] ubuntu recon-all

why do you have to use sudo to run recon-all? On Tue, 18 Dec 2007, Roberto Roiz Ssantiáñez wrote: Dear all, I have just installed freesurfer-Linux-rh9-stable-pub-v4.0.2-full.tar.gz on Ubuntu 7.10. I have tried to test the installation and after sorting out some problems with the video card dr

[Freesurfer] ubuntu recon-all

Dear all, I have just installed freesurfer-Linux-rh9-stable-pub-v4.0.2-full.tar.gz on Ubuntu 7.10. I have tried to test the installation and after sorting out some problems with the video card drivers, I obtain the following message when trying to run "recon-all -s bert -autorecon1": *roberto-des