Re: [Freesurfer] Error: cannot open libXss.so.1?

I had this same problem running on a cluster, if you can get your sysadmin to install: libXScrnSaver It should fix it. Good luck, -Sam On 13/12/2009 2:32 PM, Nick Schmansky wrote: > i'm guessing from the 'compute-0-1.local' bit of your output that this > was run on cluster, which probably doesnt

[Freesurfer] Recon error: Talairach Failure Detection

Hi, I'm getting an error trying to run a reconstruction. I'm working on multnomah and my subjects directory is: /autofs/space/multnomah_002/users/Cashlab/ *I'm using the following command:* [multnomah:Cashlab] (nmr-std-env) recon-all -autorecon1 -autorecon2 -subject MG15_SurferOutput -i MG15/MG

Re: [Freesurfer] Co-registration in FS

Can you send the reg-feat2anat log file? doug Xinian Zuo wrote: > Hi FSers, > > I am new to freesurfer. now start to use it for looking at struc-func > relationship. Normally, in fsl, I employ bet for both example_func and > highresh anat. it means that the func_brain and anat_brain are fed >

Re: [Freesurfer] Recon error: Talairach Failure Detection

Hi Rodrigo, first check the talairach registration to see whether it really failed or not -- the automatic checker is often a bit conservative. If it did, then you can fix it by hand. If it did not, then you can re-run recon-all with -notal-check. doug Rodrigo Zepeda wrote: > Hi, > > I'm getti

[Freesurfer] Using segmentation for wm/pial edits

Though the pial surface and wm surface follow expected course, there are some regions that are misclassified when the colortable is overlaid. Please see the example below... Should I worry? Thanks in anticipation LKP ___ Lena Palaniyappan Clini

Re: [Freesurfer] Using segmentation for wm/pial edits

no, that's just an (expected) mismatch between the surface-based and volume-based analyses On Mon, 14 Dec 2009, Lena Palaniyappan wrote: > Though the pial surface and wm surface follow expected course, there are > some regions that are misclassified when the colortable is overlaid. Please > see t

Re: [Freesurfer] func2roi-sess bug?

Dear experts, I was able to coax out a little bit more information on the nature of the error that I am encountering in func2roi-sess. Looking at the last line of the log (final 25 or so lines of the log are pasted below), it seems that the program is looking for bold/007/fmcsm8, but actually s

Re: [Freesurfer] func2roi-sess bug?

Ok - I believe I figured out the problem, but I wanted to post it to the list, so that anyone else who encounters this error can hopefully spend less time than I did tracking down the culprit! Essentially, a break was being passed inappropriately to the mri_vol2roi subroutine called by func2roi

[Freesurfer] QDEC error

I am trying to use qdec but it gave me this error. I don’t understand what is wrong because it read the diagnosis factor level of COS & NV but then says subject 00308 has invalid level of COS in diagnosis column. Any ideas? CHP-MP2:freesurfer brianweisinger$ qdec & [1] 7902 CHP-MP2:freesurfer

[Freesurfer] SetUp file error

Hi there, I moved my data to a new computer with Freesurfer installed. When i run the SetUpFreeSurfer.csh (or .sh for that matter) i get a strange configuration: Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/ FSFAST_HOME /usr/local/freesurfer

[Freesurfer] pediatric template vv. scaling or parcellation?

Hello - We are planning to use freesurfer in a study of 2-5year olds; I understand from previous posts that image intensity should be ok at this age range, but was wondering whether there are issues related to scaling or parcellation such that it would still be optimal to use a pediatric tem

[Freesurfer] qdec output

Hi, there, Does anyone can give me link or paper which explains all the QDEC output file, such as F.mgh, gamma.mgh, beta.mgh ... What are they, how are they related? Thanks a lot! Guang __

Re: [Freesurfer] qdec output

Try running mri_glmfit with the --help option. QDEC runs mri_glmfit. doug Guang Zeng wrote: > Hi, there, > > Does anyone can give me link or paper which explains all the QDEC > output file, such as F.mgh, gamma.mgh, beta.mgh ... > What are they, how are they related? > > Thanks a lot! > Guan

Re: [Freesurfer] SetUp file error

Hi Ilana The double slashes shouldn't matter. What does it say when you give tkmedit bert brainmask.mgz in the freesurfer environment ( i.e. after you run SetUpFreeSurfer.csh ) Krish On 12/14/09 5:27 PM, Ilana Hairston wrote: > Hi there, > I moved my data to a new computer with Freesurfer inst

Re: [Freesurfer] qdec output

Hello, Doug, Thanks a lot! I got most of them from the mri_glmfit --help except one, which is maxvox.dat. Is it a way to load this file in tksurfer? Thanks a lot! Guang > Date: Mon, 14 Dec 2009 18:35:39 -0500 > From: gr...@nmr.mgh.harvard.edu > To: freesurfer...@hotmail.com > CC: freesurfer@

Re: [Freesurfer] pediatric template vv. scaling or parcellation?

Hi Rhoshel, we haven't looked at ton at that age range, but from 5-10 we've found no need for special scaling or any age effect in registration/parcellation. cheers, Bruce On Tue, 15 Dec 2009, Rhoshel Lenroot wrote: > Hello - > > We are planning to use freesurfer in a study of 2-5year olds; I >

Re: [Freesurfer] qdec output

The maxvox.dat is just a text file that stores the voxel with the largest value. Not too useful. doug Guang Zeng wrote: > Hello, Doug, > > Thanks a lot! I got most of them from the mri_glmfit --help except > one, which is maxvox.dat. > Is it a way to load this file in tksurfer? > > Thanks a lo