Re: [Freesurfer] TRACULA trac-all -path ERROR

Hi Fernando - You need to provide you bvecs and bvals files explicitly in your configuration file. The first error occurs b/c these files are missing. a.y On Thu, 11 Oct 2012, Fernando Ventrice wrote: Yes, of course. Here I send it. Best regards, Fernando __

Re: [Freesurfer] TRACULA trac-all -path ERROR

Hi Fernando - Can you please send your scripts/trac-all.log file? My guess is something went wrong earlier in the process that caused those files not to be created. Thanks, a.y On Thu, 11 Oct 2012, Fernando Ventrice wrote: Dear Freesurfer-Tracula users, I'm trying to use Tracula to analyze

Re: [Freesurfer] TRACULA: multiple bvecs files in one configuration file

Hi Joy-Loi - No, all updates that happened since the 5.1 release are listed here: http://www.freesurfer.net/fswiki/Tracula For now it's assumed that all your subjects were scanned with the same protocol, which is usually the case, unless you're comparing different protocols. If you wan

[Freesurfer] Which atlas to use for optimal parcellation of the auditory cortex (HG and of the PT )?

Dear all, dear Christophe Destrieux, 1. I would like to know which is the best version of freesurfer to use, or rather regarding the best atlas to call (using a flag) in order to ensure that our parcellation of the auditory cortex, and of the first transverse temporal gyrus and of the planum t

Re: [Freesurfer] basic comparison

Yea, it won't allow DOF=0. Instead, you can just take the difference with mri_concat --paired-diff rh.Hybridversustrio_fsgd.sm20.mgh --o diff.mgh doug On 10/11/2012 12:02 PM, Jacobs H (NP) wrote: > That's all I have :): > > Thickness_GLM_qcache.csh --target fsaverage --fwhm 20 --slope dods --con

Re: [Freesurfer] basic comparison

That's all I have :): Thickness_GLM_qcache.csh --target fsaverage --fwhm 20 --slope dods --contrast contrast_1_-1.mat --glm_dir /Volumes/HEIDI2/comparingTrioHybrid/GLM_DIR --fsgd_dir /Volumes/HEIDI2/comparingTrioHybrid/FSGD --fsgd fsgd.Hybridversustrio_fsgd.txt contrast_1_-1.mat argv: Subscript

Re: [Freesurfer] basic comparison

can you send the full terminal output? On 10/11/2012 11:56 AM, Jacobs H (NP) wrote: > Hi Doug, > > This is from the log file: > > > mri_glmfit --y lh.Hybridversustrio_fsgd.sm20.mgh --fsgd > /Volumes/HEIDI2/comparingTrioHybrid/FSGD/fsgd.Hybridversustrio_fsgd.txt dods > --glmdir lh.Hybridversustri

Re: [Freesurfer] basic comparison

Hi Doug, This is from the log file: mri_glmfit --y lh.Hybridversustrio_fsgd.sm20.mgh --fsgd /Volumes/HEIDI2/comparingTrioHybrid/FSGD/fsgd.Hybridversustrio_fsgd.txt dods --glmdir lh.Hybridversustrio_fsgd.dods.20.glmdir --surf fsaverage lh --C /Volumes/HEIDI2/comparingTrioHybrid/GLM_CONTRAST.M

Re: [Freesurfer] basic comparison

what's your command line and resulting terminal output? On 10/11/2012 11:49 AM, Jacobs H (NP) wrote: > Hi Doug, > > Thanks for your help. I just ran the mri_glmfit the way you suggested. But > FreeSurfer does not provide me a contrast directory and no gamma.mgh. It only > gives me a mask.mgh, Xg

Re: [Freesurfer] basic comparison

Hi Doug, Thanks for your help. I just ran the mri_glmfit the way you suggested. But FreeSurfer does not provide me a contrast directory and no gamma.mgh. It only gives me a mask.mgh, Xg.dat and the mri_glmfit.log? Any ideas what might have gone wrong? Thanks! Heidi

Re: [Freesurfer] basic comparison

Hi Heidi, the easiest way is probably to do the analysis with mri_glmfit specifying that each subject is it's own group and a contrast to compute the difference between the groups.The gamma.mgh in the contrast directory will be the thickness difference between the two subjects. There will be a

[Freesurfer] Cognitive Neuroscientist Position, University of Nebraska, Lincoln (fwd)

-- Forwarded message -- Date: Thu, 11 Oct 2012 13:29:03 + From: Nicole Earnest To: "freesurfer-ow...@nmr.mgh.harvard.edu" Subject: Cognitive Neuroscientist Position, University of Nebraska, Lincoln Please forward the following job ad to your listserv. Thank you. Cog

[Freesurfer] MR Physicist/Scientist Position, University of Nebraska, Lincoln (fwd)

-- Forwarded message -- Date: Thu, 11 Oct 2012 13:28:06 + From: Nicole Earnest To: "freesurfer-ow...@nmr.mgh.harvard.edu" Subject: MR Physicist/Scientist Position, University of Nebraska, Lincoln Please forward the following job ad to your listserv. Thank you. MR Ph

Re: [Freesurfer] Control point edits adversely affect cortical surfaces using FS 5.1

Hi Vanessa if you can upload an example (the entire subject dir) before adding the single control point you refer to, and after adding it we'll track it down. thanks Bruce On Thu, 11 Oct 2012, Vanessa Louise Cropley wrote: > Hi all, > > I have seen others post a similar problem on the frees

Re: [Freesurfer] Boundary problem

Hi Youngmin that looks like there must be a big topological defect causing your problem. If you can't find it, feel free to upload your dataset and we'll take a look Bruce On Thu, 11 Oct 2012, youngmin huh wrote: > Dear all, > > I'm working with some 3T images and got some bad segmentation p

[Freesurfer] basic comparison

Hi FreeSurfers, I am preparing a simple presentation, to show some basic stuff in my lab and therefore I would like to compare the cortical thickness of two subjects. Is there a way to do this? For the GLM, I probably have not enough degrees of freedom? Is there a way that I could subtract the t

Re: [Freesurfer] cortical parcellation question

Hi Daniel, no, sorry. The gca is not a cortical atlas. Those labels are stored in the .gcas file and aren't in the same space (in fact, they are in a surface-based spherical coordinate system and not in the volume at all, so not easily combinable). Bruce On Thu, 11 Oct 2012, Daniel Ferreira

[Freesurfer] TRACULA: multiple bvecs files in one configuration file

Hello, I see in the message thread that as of July 2011 there was no support for multiple bvecs files in one configuration file. Have any changes been made regarding this? And if so, how can I include multiple paths to bvecs files? Thank you, Joy-Loi _