[Freesurfer] problems

Hi, I had downloaded the freesurfer to my system (Linux Fedora Core 4) and had completed all the installation procedures. Question 1: I would like to convert analyze format to .mgz. What command line do I use? Can I type "mri_convert x249.img 001.mgz "? Question 2: When I type "recon-

RE: [Freesurfer] problems

1) Yes. mri_convert x249.img 001.mgz 2) It's missing libstd++.so.5. I suggest you run find / -name "libstd*" -print If you find a libstd++.so.6 for instance create a libstd++.so.5 as a symbolic link. 3) It's ok. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] mgh.harva

Re: [Freesurfer] problems

Use the centos4 build of freesurfer with fedora core 4. it uses libstdc ++.so.6. On Thu, 2007-10-04 at 16:30 +0800, 顏鳳賢 wrote: > Hi, > > I had downloaded the freesurfer to my system (Linux Fedora Core 4) > and had completed all the installation procedures. > > Question 1: > > I would like

[Freesurfer] using the talairach_with_skull.lta transform

Hello, We are doing a reproducibility study and have found a different ICV for the same subject. I am trying to check the registration of nu_noneck.mgz to RB_all_withskull_2006-02-15.gca. I believe it is probably a registration problem. Which freesurfer binary would I use to apply the talaira

Re: [Freesurfer] using the talairach_with_skull.lta transform

mri_convert --apply_transform should work, or you can just load it in tkmedit On Thu, 4 Oct 2007 [EMAIL PROTECTED] wrote: Hello, We are doing a reproducibility study and have found a different ICV for the same subject. I am trying to check the registration of nu_noneck.mgz to RB_all_withskul

Re: [Freesurfer] using the talairach_with_skull.lta transform

Chris, You might also try: tkregister2 \ --targ $FREESURFER_HOME/subjects/fsaverage/mri/T1.mgz \ --mov nu_noneck.mgz \ --lta transforms/talairach_with_skull.lta \ --reg register.dat which would show you the alignment between nu_neck.mgz and fsaverage, which is already talairach aligned. The r

[Freesurfer] Re: Error: Cannot allocate memory

Hi Chris, Can you forward me to the person I could ask about this issue? I've been running jobs the same way using freesurfer for months and today I keep gettting this error message: Cannot allocate memory i.e. mri_convert orig.mgz ./tmp.mri_nu_correct.mni.29819/nu0.mnc mri_convert orig.mgz ./tm

RE: [Freesurfer] parcellation problem

I did not run the autorecon3 before I checked the parcellation. Thank you, Xin From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Tue 9/11/2007 11:33 AM To: Wang, Xin Cc: freesurfer Subject: RE: [Freesurfer] parcellation problem that type of pattern usually

[Freesurfer] model for pair-T test

Hello, group, Could anybody tell me how to do the pair T test and the repeat measurement F test? I will really appreciate if you can share the steps and GLM of the tests. I am using the old freesurfer group analysis. Thank you, very much, Xin Wang _

[Freesurfer] help on installation under VMWARE + suse 10.2

hi-I am trying to install freesurfer my computer with the following settings: Operating system: Win XP Open Suse10.2 running under vmware workstation 6.0. Display card: NVIDIA Quadro FX 3400/4400. The problem I have is that the tksurfer doesn't work well, like what's described on the wiki, onl

Re: [Freesurfer] Re: Error: Cannot allocate memory

I am also getting the same error as below. > Hi Chris, > > Can you forward me to the person I could ask about this issue? > > I've been running jobs the same way using freesurfer for months and today > I keep gettting this error message: Cannot allocate memory > > i.e. > mri_convert orig.mgz ./tm

Re: [Freesurfer] Re: Error: Cannot allocate memory

t; > > Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.0.1-20071004 > > > > RedHat release: CentOS release 4.4 (Final) > > > > Kernel info: Linux 2.6.9-42.0.3.ELsmp x86_64 > > > > NMR Center info (/space/freesurfer exists): > > > > machin

Re: [Freesurfer] Re: Error: Cannot allocate memory

/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.0.1-20071004 RedHat release: CentOS release 4.4 (Final) Kernel info: Linux 2.6.9-42.0.3.ELsmp x86_64 NMR Center info (/space/freesurfer exists): machine: galen SUBJECTS_DIR: /autofs/space/galen_002/users/carl/S4_HR_LR18

[Freesurfer] previous FS versions

Hello, Is it possible to get a version of Freesurfer other than the most current? In particular, I'm interested in getting a copy of v3.0.5 for the CentOS (RHEL 4) Linux platform. thanks, Mike H. -- Michael Harms, Ph.D. Conte

[Freesurfer] reference for annotation

Hi, If we use the old version of aparc for parcellation (the older default, as opposed to aparc.a2005s), what should we cite in a paper? Thanks, Rob -- Robert P. Levy, B.A. Research Assistant, Manoach Lab Massachusetts General Hospital Charlestown Navy Yard 149 13th St., Room 2611 Charlestow

[Freesurfer] TkmEdit message

Hi, When I run tkmedit, I receive the following message. It doesn't seem to affect the functionality. Could you explain why this message shows up. Xlib: extension "XFree86-DRI" missing on display ":0.0". Thanks, Anil. ___ Freesurfer mailing list Free

Re: [Freesurfer] reference for annotation

our Cerebral Cortex paper On Thu, 4 Oct 2007, Robert Levy wrote: Hi, If we use the old version of aparc for parcellation (the older default, as opposed to aparc.a2005s), what should we cite in a paper? Thanks, Rob ___ Freesurfer mailing list Fre

Re: [Freesurfer] previous FS versions

Mike, I've posted v3.0.5 for centos and centos_x86_64 here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/stable Nick On Thu, 2007-10-04 at 16:08 -0500, Michael Harms wrote: > Hello, > Is it possible to get a version of Freesurfer other than the most > current? > In particular