[Freesurfer] trouble with longitudinal processing in FS5.1

Hello FreeSurfer community, I am running into a problem with my longitudinal data in the new FS5.1 and am wondering if anyone else has run into this error message during the unbiased template creation. I have 4 scans from 2 subjects and have run into the same error at the same place. I only run

[Freesurfer] recon-all exicted with ERROR

Dear All, I just installed my new FS version (I saved my old version under freesurfer_backup). I am getting an error when I am running recon-all on my GNU/LINUX.Do I need a license file before running? What steps I need to follow before running the new FS version? Here is the outcome:

Re: [Freesurfer] recon-all exicted with ERROR

You do need a license. You can just copy the old one into the new directory. doug Antonella Kis wrote: Dear All, I just installed my new FS version (I saved my old version under freesurfer_backup). I am getting an error when I am running recon-all on my GNU/LINUX.Do I need a license file

Re: [Freesurfer] Two timepoints - same subject, correlation matrix

On Jun 17, 2011, at 6:25 PM, Sudhin A. Shah sut2...@med.cornell.edu wrote: Hi, Can somebody please help me figure out how to correct this issue? 1 subject - 2 functional scans 1) run recon-all on subject anatomical. 2) process functional series (using AFNI/FSL) - each

Re: [Freesurfer] trouble with longitudinal processing in FS5.1

i'm guessing it might be a memory issue. registering 4 scans takes a lot of memory. how much memory have you dedicated to your virtual machine? we recommend at least 4GB. n. On Tue, 2011-06-21 at 09:59 -0500, Jane Lawrence wrote: Hello FreeSurfer community, I am running into a problem with

Re: [Freesurfer] Two timepoints - same subject, correlation matrix

Hi Sudhin, this looks like an AFNI question. Have you tried posting to the AFNI list? doug Sudhin A. Shah wrote: On Jun 17, 2011, at 6:25 PM, Sudhin A. Shah sut2...@med.cornell.edu mailto:sut2...@med.cornell.edu wrote: Hi, Can somebody please help me figure out how to correct this

[Freesurfer] PETSC ERROR

Hi I posted a couple days ago about a PETSC ERROR with while running mri_cvs_register but I seem to be having a more general problem. I'm receiving the same error on two 10.6.7 macs as well as on a Windows running virtualbox, both while processing my own subjects and FS5.1 bert. I'm using the

[Freesurfer] launchpad help

Hello, I am trying to do recon-all using launchpad, and I am not sure how to fix the error I am getting. I checked IT's launchpad help website, but can't seem to figure it out. Using fs v4 subjects_dir: /space/ventzl/36/users/RespMon12C/subjects command: pbsubmit -q sergeant -l nodes=1:opteron

Re: [Freesurfer] launchpad help

What exact website page are you using for help on launchpad? launchpad has no opteron nodes so you should not be specifying that resource. Its queue names are also different than seychelles. There is no sergeant queue. Read: https://www.nmr.mgh.harvard.edu/martinos/itgroup/launchpad.html

Re: [Freesurfer] error during mri_cvs_register

Hi David, FreeSurfer's binaries for MAC are still 32-bit and apparently cvs tries to allocate more that is possible. The lines of the error code below suggest that. I had the same problem and had to opt for x86_64 linux binaries, where the cvs runs fine. It needs ~ 6 GB of memory and takes ~ 2

Re: [Freesurfer] error during mri_cvs_register

Is there a reason that the Mac binaries are not available in 64-bit versions? On Jun 21, 2011, at 3:11 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Date: Tue, 21 Jun 2011 21:11:54 +0200 From: Martin Kavec martin.ka...@gmail.com Subject: Re: [Freesurfer] error during mri_cvs_register To:

[Freesurfer] mask conversion from talairach

Hello Freesurfers, Using FS 4.5, I am attempting to do an ROI analysis based on activations seen in the group contrast. I'd like these ROI's to be a sphere around the peak voxel of each activation. Using a matlab program written by a colleague, I was able to generate spherical masks around the