Re: [Freesurfer] [recon-all] [MacOS Leopard] Global Region of the brain empty

if you run them one at a time does it still happen, or only if you are running 8 in parallel? Feel free to drop it on our ftp site so we can take a look. Bruce On Mon, 5 Jan 2009, Pedro Paulo de Magalhães Oliveira Junior wrote: Hi, I'm running 100 cases in a MacPro with 8 core and in al

[Freesurfer] unpacking err runs

Hello, I am unpacking recent functional data and during a function run we needed to stop it early and so now when I view it in unpacksdcmdir, it has a err next to the run. Since those runs are typically skipped when unpacking, is it possible to override that and download the file anyway? Any help

Re: [Freesurfer] unpacking err runs

Try adding -unpackerr Adrienne McCallister wrote: Hello, I am unpacking recent functional data and during a function run we needed to stop it early and so now when I view it in unpacksdcmdir, it has a err next to the run. Since those runs are typically skipped when unpacking, is it possibl

Re: [Freesurfer] Problem with post-spm registered data

Hi Dave, I'm not sure where to begin with this. Can you give more info? In particular, you might look at surfer.nmr.mgh.harvard.edu/fswiki/BugReporting for ways to report issues efficiently. doug Dave Brohawn wrote: Hello, Josh Roffman and I recently ran an fMRI scan. Our subject's data vi

Re: [Freesurfer] vertex/talairach coordinates

yes, it is Bruce Fischl wrote: actually Doug can confirm, but I think the average surface RAS are already Talairach coords On Wed, 24 Dec 2008, Nick Schmansky wrote: Corey, I'm not 100% sure how to do this but a starting point is to use mris_info on the surface file you are getting coordina

Re: [Freesurfer] questions about region-wise analysis data

Siddharth Srivastava wrote: Hi all, I am trying to understand the --surf flag in the mri_glmfit command, and the 2 parameters that follow it. The tutorial mentions --surf average lh . 1) what should "average" contain? should it point to the average of the population, of fsaverage, or

RE: [Freesurfer] Problem with post-spm registered data

Sorry for asking same question here again. I asked Dung before holiday about the criteria of good registration of fMRI and thickness map. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg08913.html I paste m

Re: [Freesurfer] mri_surfcluster problem?

Hi Lauren (and Doug), I'm having the same issue. I ran montecarlo simulations on Friday and then tried to use the results in mri_surfcluster. It ran, but I also got the same CWP values (-0.1) for each cluster in the sum file. Also, when it runs, it gives a CEPHES ERROR. Here is what I get

RE: [Freesurfer] questions about region-wise analysis data

I want to ask a related question: We study group differences between patients and controls, and correlations of symptoms and thickness in patients only. We would like to display (and extract) the common regions between two analyses in ONE figure. Which template can we use? We created two sets of

[Freesurfer] How to overlap FSL statistical map onto surface in Matlab?

Hi I was able to view the statistical maps (from FSL) on the subject's surface following the tutorial (FsTutotial/FSLFeatFreeSurfer). I would like to see the same image in Matlab. I could show the subject's surface as well as the the cortical parcellation in Matlab by modifying the functi

RE: [Freesurfer] questions about region-wise analysis data

hmmm, you should be able to display any of the average RIOs on any of the surfaces as they should all have the topology of ic7. What exactly fails? On Mon, 5 Jan 2009, Wang, Xin wrote: I want to ask a related question: We study group differences between patients and controls, and correlatio

[Freesurfer] [recon-all] [MacOS Leopard] Global Region of the brain empty

Hi, I'm running 100 cases in a MacPro with 8 core and in all cases I'm receiving this message in skull strip step: GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1073732725 RIGHT_CERCSF_MIN=1, CSF_intensity=2, CSF_MAX=218 , nb = -1073752790 LEFT_CER CSF_MIN=0, CSF_inten

[Freesurfer] QDEC on multiple datasets

Hello, I have run qcache on two separate datasets, and now would like to combine them and look at the data using QDEC. What is the proper way to go about doing this? Will I need to run an entirely separate instance of qcache on all of the datasets at once? Thanks for any information! ___

Re: [Freesurfer] QDEC on multiple datasets

As long as you used the same version of freesurfer and the same average subject (fsaverage, typically) for both runs of qcache, then there should be no problem to combine the two datasets. Nick On Mon, 2009-01-05 at 15:03 -0600, nels5...@umn.edu wrote: > Hello, > > I have run qcache on two sepa

Re: [Freesurfer] How to overlap FSL statistical map onto surface in Matlab? (fwd)

Hi Thanks for the reply. I think all I need are the vertices and faces of a image to show it in Matlab. I can get the vertices and faces of lh.inflated and lh.aparc.annot of the subject. I do not know how to get the vertices and faces of zstat1.nii.gz generated by FSL of the same subject?

Re: [Freesurfer] How to overlap FSL statistical map onto surface in Matlab? (fwd)

Have you tried registering the volumetric data to the surface? Flirt will do this, or Doug's very nice new bbregister tool. cheers, Bruce On Mon, 5 Jan 2009, Yunjie Tong wrote: Hi Thanks for the reply. I think all I need are the vertices and faces of a image to show it in Matlab. I can get