Re: [Freesurfer] bvecs error from Tracula

Hi ZeKe, I am getting this error during Tracula procedure somewhere between bbregister! BR On Jul 24, 2013 5:42 PM, Z K zkauf...@nmr.mgh.harvard.edu wrote: Hello Amir, According to the log file you've attached, recon-all finished to completion without any errors. Are you sure you are

[Freesurfer] R: Re: R: Re: problem with nu_correct

Normal 0 14 false false false IT X-NONE X-NONE MicrosoftInternetExplorer4 Hello Zeke, I must make a clarification: I use freesurfer on a PC cluster. I have

Re: [Freesurfer] different results between 5.1.0 and 5.2.0

Hi Clarissa have you visually inspected them? Does one version look more accurate than another to you? We do system tests on things like subcortical volumes before releasing a version and our tests show that the accuracy in these structures has not changed, so I'm not sure what the source of

Re: [Freesurfer] different results between 5.1.0 and 5.2.0

yes, definitely for cortical surfaces Bruce On Thu, 25 Jul 2013, Watson, Christopher wrote: I don't know, but I'm pretty sure the Freesurfer team will recommend you use v5.3.0. There are emails saying as much. Chris From:

Re: [Freesurfer] different results between 5.1.0 and 5.2.0

Thank you for your reply! I will try to run the new version, and also try to see what is the source for such differences. I guess the new release is the easiest solution. clarissa 2013/7/25 Bruce Fischl fis...@nmr.mgh.harvard.edu yes, definitely for cortical surfaces Bruce On Thu, 25 Jul

[Freesurfer] FreeSurfer Version

Is there any other way I can find the FreeSurfer version I am using? According to https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.HowdoIknowtheversionofFreeSurferI.27mrunning.3F I have to run: recon-all -version, but I get the output below. Now the stable FreeSurfer Version is

[Freesurfer] bug reporting

Hello, I've received the following error using Ubuntu 13.04: WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! ERROR: cannot find subj001.nii.gz Linux neuron 3.2.0-49-generic #75-Ubuntu SMP Tue Jun 18 17:39:32 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s exited with

Re: [Freesurfer] bvecs error from Tracula

Hi Amirhossein - If your error happens when bbregister is run, then it's not the error that the dmri_5.1_snow_leopard.tar.gz fix was meant to address. In any case that fix is not relevant to you b/c you're using 5.3 and not 5.1. Can you please send your trac-all.log to establish where

Re: [Freesurfer] FreeSurfer Version

look at $FREESURFER_HOME/build-stamp.txt doug On 7/25/13 11:45 AM, Rodrigo Perea wrote: Is there any other way I can find the FreeSurfer version I am using? According to https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.HowdoIknowtheversionofFreeSurferI.27mrunning.3F I

Re: [Freesurfer] bug reporting

Does subj001.nii.gz exist in the folder you ran recon-all from? On 7/25/13 12:21 PM, Kyllo, Hannah M wrote: Hello, I've received the following error using Ubuntu 13.04: WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! ERROR: cannot find subj001.nii.gz Linux neuron

[Freesurfer] need help

Hi there, I was trying to learn the freesurfer, I have hard time to download at the  beginning, later after that, I also have no knowledge of how to import images and analyse them. I really need your help tremendously. Thanks, Haielom___ Freesurfer

[Freesurfer] MRI_Convert error

Hello, I am resending this post since there is no reply for 2 days, I really appreciate your help. thanks so much. I have several errors using mri_convert to convert 3T Philips T1-wt, DTI and fMRI images. The last one on T1-wt images tells me to send email to freesurfer, so here is the error

[Freesurfer] functional connectivity, group averages

Hi Team, I have a question on making a group average of subjects for functional connectivity. In detail, I want to make a surface overlay that is the average correlation (r-value) of a certain subject group. What commands would be used for this? simply isxconcat-sess? I could not find much info on

Re: [Freesurfer] need help

Hi Haielom have you read any of the documentation or tuturials? Look at the usage of recon-all and start there. It's pretty simple to get started - just give the recon-all script one file in a high-resolution T1-weighted dicom series like an mprage. cheers Bruce On Thu, 25 Jul 2013, Haielom

Re: [Freesurfer] MRI_Convert error

Hi Pom are these the dicoms straight off your Philips scanner? We don't have a ton of experience with philips. Maybe you could use something else to convert them to NIFTI, like MRIcron, then pass them to us? cheers Bruce On Thu, 25 Jul 2013, Pom Sailasuta wrote: Hello, I am resending

Re: [Freesurfer] MRI_Convert error

Hi Bruce, OK, thanks. I will try MRIcron. Pom On Thu, Jul 25, 2013 at 7:59 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Pom are these the dicoms straight off your Philips scanner? We don't have a ton of experience with philips. Maybe you could use something else to convert them

[Freesurfer] Segmentation edits

Hi all, I am doing cortical thickness and surface area analyses and had a few questions regarding editing the borders. 1) Is it reasonable to edit every (big and small) error that I find? Basically, how much a difference would it make in terms of the surface area and cortical thickness values if

Re: [Freesurfer] bug reporting

Do you have permissions to the file? If so, rerun recon-all with -debug as the first option, then send the terminal output to the list. doug ps. Please send emails to the list and not to us individually. thanks! On 7/25/13 2:31 PM, Kyllo, Hannah M wrote: yes - Hannah Kyllo

[Freesurfer] are many *.dat files written out to disk in subj_dir/mri and then deleted when autorecon completes?

After importing a subject's data (T1 single time point) I run a script with these commands: recon-all -s subject -autorecon1 recon-all -s subject -autorecon2 recon-all -s subject -autorecon3 I did this twice, once on each of two linux machines. I am using the same exact input intensity T1 data