Re: [Freesurfer] FreeSurfer & Ubuntu 11.10

Hi Ian, Thanks for the information. So I followed your instructions carefully with the same result (I modified the terminal options as well). I also modified it as well to see if I can get it working but to no avail. Here is the contents of my .tcshrc file: #.tcshrc # User specific aliases

Re: [Freesurfer] FreeSurfer & Ubuntu 11.10

Hi Brian I had to change the terminal config for it to use tcsh. I think Ubuntu now uses The Debian Almquist shell (dash) and I have had problems running freesurfer from it. install tcsh using aptitude and then in the preferences of your terminal (Edit > profile preferences) in the tab "title

Re: [Freesurfer] FreeSurfer & Ubuntu 11.10

That is what I did...my path is /usr/local/freesurfer However, mine doesn't seem to work. Brian. From: Martijn Steenwijk [mailto:martijnsteenw...@gmail.com] Sent: December-30-11 2:37 PM To: James, Brian Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] FreeSurfer & Ubuntu 11.10 Ju

Re: [Freesurfer] FreeSurfer & Ubuntu 11.10

Just untarring the .tar.gz in /usr/local like documented here (http://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall) works like a charm on Ubuntu 11.10. Best, Martijn Van: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens James, Brian Verz

[Freesurfer] FreeSurfer & Ubuntu 11.10

Hi Everyone, I thought I would try installing FreeSurfer on Ubuntu because I was having so many issues trying to install Octave on CentOS. On the bright side, Ubuntu can download Octave directly from the repository. The downside is when I test my freesurfer install with tkmedit

Re: [Freesurfer] Registration Error

Hi Antonella, > I have a problem with mri_cvs_register. I am getthing the following error and > I will be very grateful if you can help me to fix it (I am don't understand > what means this errors). I suspect that you are running out of memory on your computer. Can you tell me the parameters

[Freesurfer] recon all problem

i looked in the .bashrc file and it is written : FREESURFER_HOME=/home/amesse/software/freesurfer5.1 ;       but  freesurfer is installed in another account to which  i have no access for the moment. i'll see it on monday thank you michael ___ Freesu

Re: [Freesurfer] aparc.a2009s+aseg problem

You said initially that you were using FS v5.1, but that recon- all.local-copy is not consistent with FS v5.1. Are you processing subjects from scratch? If so, then you need to check your path/environment and figure out why an older version of recon-all is being called when you think that you're

Re: [Freesurfer] fixing hemisphere leakage

You could also look at the filled.mgz to see if the hemis are separated and potentially make some edits. Then you would run: recon-all -tessellate -smooth1 -inflate1 -qsphere -fix -white -smooth2 -inflate2 -autorecon3 -s Lastly, you could set seed points for the corpus callosum using the -cc

[Freesurfer] Registration Error

Hi, I have a problem with mri_cvs_register. I am getthing the following error and I will be very grateful if you can help me to fix it (I am don't understand what means this errors). Also, after running a group analysis with mri_glmfit-sim and using the option --grf (so I have the survining

Re: [Freesurfer] aparc.a2009s+aseg problem

For some reason the beginning section of the recon-all.log that you sent is missing (i.e,. the part containing the actual command that you ran). What was the exact recon-all command that you used? From the log file, only the very first mri_convert was performed. Was your command perhaps recon-al