Re: [Freesurfer] Pial surface volume

Dear FreeSurfer developers I couldn't find the mentioned mris_volume in the commands. Shall i use mri_vol2surf or something? Looking forward to hearing from you! On Tue, Sep 5, 2017 at 9:46 AM Fereshte wrote: > Hi Bruce, > Thank you for your replies. > Cheers > > On

Re: [Freesurfer] Freeview aborts under centos6

Thanks, I gave this to the system admin as I do not ave the sudo rights. I’ll come back! Best, Markus > On 15 Sep 2017, at 20:06, Hoopes, Andrew wrote: > > Hm okay thanks - I’m curious what happens when you run: > > cd $FREESURFER_HOME/lib/vtk/lib/vtk-5.6 > # backup

Re: [Freesurfer] Freeview aborts under centos6

Hm okay thanks - I’m curious what happens when you run: cd $FREESURFER_HOME/lib/vtk/lib/vtk-5.6 # backup the shared objects mv libvtkverdict.so libvtkverdict.so.bk mv libvtkverdict.so.5.6 libvtkverdict.so.5.6.bk # link them to 5.6 ln -s libvtkverdict.so.5.6.0 libvtkverdict.so ln -s

[Freesurfer] mixed-design with fs-fast

Hi list, I have 3 groups and two measure of rest-state at different time (baseline and t1).Using FS-FAST, I would look at:1-crossectional differences between groups (at baseline and T1)2- within group, the longitudinal differences between the conditions.Is possible to use a mixed-design with

Re: [Freesurfer] Freeview aborts under centos6

Dear Andrew, The command gives this result: [gschwind@login1 ~]$ /sbin/ldconfig -N -v $(sed 's/:/ /' <<< > $LD_LIBRARY_PATH) | grep libvtkverdict.so > /sbin/ldconfig: Can't stat > /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.71.x86_64/jre/lib/amd64/server: No > such file or directory > /sbin/ldconfig:

[Freesurfer] how to get the volume of the complete ventricle system ?

dear all, Ive tried to get the volume of the ventricle system by using two different calculations. first of all i tried to get the volume by: brainsegvol - brainsegvolnotvent than i tried to simply add all the seprate parts of the ventricle system (rh lat ventricle + lh lat ventricle + 3rd,

Re: [Freesurfer] Freeview aborts under centos6

Hi Markus, What is the output when you run the following: (this will list libraries you have access to) /sbin/ldconfig -N -v $(sed 's/:/ /' <<< $LD_LIBRARY_PATH) | grep libvtkverdict.so best, Andrew On Sep 15, 2017, at 3:33 AM, Markus Gschwind

[Freesurfer] Running statistical analysis on surface data in R

Dear FreeSurfer users, I am using R to apply a statistical method on surface data registered to fsaverage (for example, left hemisphere area smoothed at bandwidth=10mm). This method requires data be in a matrix Y with NS rows and V columns, where NS = #subjects and V=#vertices. The output

[Freesurfer] Freeview aborts under centos6

Dear experts, I am installing freeusrfer on our cluster which is running Centos6. [gschwind@login1 ~]$ uname -a Linux login1.cluster 2.6.32-696.1.1.el6.x86_64 #1 SMP Tue Apr 11 17:13:24 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Freeview aborts without any other complaint. [gschwind@login1 ~]$

[Freesurfer] Longitudinal processing -qcache ERROR

Hi everyone, During my PhD, I'm using some longitudinal data and at the setp called "BASE" but when i want to make a qcache processing with the last version of FreeSurfer (i.e. 6.0)(command used : "*recon-all -base template_1-02 -qcache*") it doesn't work. I have a error message : "Error : cannot

[Freesurfer] Freeview aborts under centos6

Hi experts, I am installing freeusrfer on our cluster which is running Centos6. [gschwind@login1 ~]$ uname -a Linux login1.cluster 2.6.32-696.1.1.el6.x86_64 #1 SMP Tue Apr 11 17:13:24 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Freeview aborts without any other complaint. [gschwind@login1 ~]$