Re: [Freesurfer] trac-all -path Help needed

2013-12-20 Thread Francesco Baldacchini
I commented out the mni_template command and all went good, Thank you so much for the help 2013/12/18 Anastasia Yendiki > > Ciao Francesco - The problem is that the pre-processing encountered an > error, so parts of it didn't actually complete: > > Image Exception : #22 :: ERROR: Could not open

Re: [Freesurfer] 3 groups and one covariate

2013-12-20 Thread Douglas N Greve
Hi Stef, there are examples there with covariates. Can you follow those? doug On 12/19/2013 05:56 PM, yashin7...@libero.it wrote: > Hi experts, > I'd like to find group difference (thickness) among 3 groups taking in account > one covariate. > I'd like to use DOSS. Is correct? I have read the guide

[Freesurfer] vertex-wise threshold and cluster-wise p values

2013-12-20 Thread Rujing Zha
Hi all, I want to know difference between vertex-wise and cluster-wise in Groupanalysis. Can I just think vertex-wise are uncorrected P-value(which is the same as voxel-wise value) and cluster-wise value are the vertex population which are survived after a specific threshold correction? Thanks.

[Freesurfer] p value in CWP colume

2013-12-20 Thread Rujing Zha
Hi all, I just study group analysis tutorial and I am confused with how to find cluster-wise probability in CWP colume(i.e 0.2 in clusterno 1). Did I need to process additinoally? Thanks. All the best. 2013-12-21 Rujing Zha School of Life Science University of Science and Technology of C

Re: [Freesurfer] vertex-wise threshold and cluster-wise p values

2013-12-20 Thread Douglas N Greve
yes, a second p-value is computed for the population (cluster) and clusters are kept if their p-value is less than a certain threshold (usually .05) doug On 12/20/2013 11:11 AM, Rujing Zha wrote: > Hi all, > I want to know difference between vertex-wise and cluster-wise in > Groupanalysis. C

[Freesurfer] Freesurfer dev install/ testing error

2013-12-20 Thread Octavian Lie
Dear All, I have ubuntu 12.4, and downloaded/installed the dev (12/19/2013) version of Freesurfer (I used previously version 5.1). Installation was uneventful, including getting the return to command > source $FREESURFER_HOME/SetUpFreeSurfer.csh FREESURFER_HOME /usr/local/fs5.3/freesurfer FSFA

Re: [Freesurfer] Freesurfer dev install/ testing error

2013-12-20 Thread Octavian Lie
I forgot to mention that I downloaded the freesurfer-Linux-centos6_x86_64-dev version (again 12/19/2013), and that other lib files, such as libjpeg.so files (related to install issues on some ubuntu systems according to the release notes) are stored in /usr/lib/x86_64-linux-gnu/ on my computer Th

Re: [Freesurfer] 3 groups and one covariate

2013-12-20 Thread yashin7...@libero.it
I'm sorry, but my difficult is due to lacking of an example with three levels/groups and one covariates. I have found a lot of example in the guide but they are referred to two levels with covariate or three levels is without covariates. Please can you check these mtx? 3 classes 1 variable co

Re: [Freesurfer] tksurfer visualization and -aseg option in tkmedit

2013-12-20 Thread Garikoitz Lerma-Usabiaga
Hi Rujing, About tksurfer visualization, we had the same problem, it was because the graphic card in the server, you cannot do anything about it (well, install a different one). If I remember correctly, you need a graphic card that supports OpenGL. Regards, Gari On Friday, December 20, 2013, Ruji