[Freesurfer] Longitudinal processing with variable time points?

Hello all, I am hoping to do some longitudinal processing on a dataset. However, the intervals between time points for each subject are not uniform. Can freesurfer's longitudinal processing stream handle this, or do all of the time points need to be equal?

Re: [Freesurfer] Longitudinal processing with variable time points?

The time between scans is not relevant to the longitudinal stream itself. You may need to model the data differently when you go to perform a statistical analysis. doug Dankner, Nathan (NIH/NIMH) [F] wrote: Hello all, I am hoping to do some longitudinal processing on a dataset. However,

[Freesurfer] optseq post-hoc sorting

Hello-- I'm designing an event-related task that does not have predefined conditions. instead, I plan to do some post-hoc sorting based on performance and stimuli characteristics. I expect that after sorting, I will have 5 conditions- but it could be more or less. Is it advisable to

Re: [Freesurfer] GM-wm error

Could be a problem with intensity normalization. Are the white matter voxels mostly 110 in the T1.mgz? Also, look at the nu.mgz. I've seen some problems where the nu_correct fails. Usually, this happens when there are a few extremely bright voxels. doug Ritobrato Datta wrote: Hello All, I

[Freesurfer] centOS vs. ubuntu

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 at the center are CentOS 5)? Also, since I need to install the OS myself, and I understand that ubuntu is easier in that respect, I'm wondering whether

Re: [Freesurfer] GM-wm error

can you send us the recon-all.log? On Mon, 7 Dec 2009, Ritobrato Datta wrote: Hello All, I ran recon-all for a subject and when I did the following to check the gray matter and white matter segmentation I found that it couldnt do it. tkmedit subjid brainmask.mgz lh.white -aux T1.mgz

[Freesurfer] recon-all exited with errors

Hi everyone, I had a recon-all exit with errors, but I can't find a specific error message that explains what the problem is. This is v4.5.0. The last several lines of the script are pasted below: Any ideas as to what went wrong? Thanks, Dana gca peak Unknown = 0.94427 ( 0) gca peak

[Freesurfer] a question about the mris_volmask ERROR

Hi, there, I have question about the mris_volmask ERROR. I ran multiple subjects on our SUN Grid Engine system. sometimes some subjects are sent to the same cluster node, and limited memory is assigned to each subject. Because of this, I often met an ERROR at the mris_volmask

[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 at

[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 at

Re: [Freesurfer] centOS vs. ubuntu

yes, freesurfer works on centos 5 (and mne should as well). if you install on ubuntu, the only change you need to make, to allow qdec to work, is: cd /usr/lib ln -s libtiff.so.4 libtiff.so.3 On Mon, 2009-12-07 at 14:56 -0500, dah...@nmr.mgh.harvard.edu wrote: Hi, Will Freesurfer and MNE

Re: [Freesurfer] VMware?

depends on how much memory you have on your machine running VMware, and what you intend to do with it. if you intend to run recon-all, you will need to dedicate about 4GB to the virtual machine. this would mean you would need at least 6GB on the machine (since Windows needs a couple GB). On

Re: [Freesurfer] VMware?

that's more than enough. remember that it is up to you to configure the vm to give it 4 or 8GB. i think it defaults to 2GB. On Mon, 2009-12-07 at 17:52 -0500, dah...@nmr.mgh.harvard.edu wrote: Thanks Nick. I have 24 GB RAM on this machine, so I should be in the clear for any process,