[Freesurfer] Extreme mean values for significant clusters (using GLM)

Dear Freesurfer Mailing List, I have just run a GLM analysis using mri_glmfit with area as the measure of interest. For each of my significant contrasts, I extracted the mean area for each subjects from the corresponding cache.th13.abs.y.ocn.dat file. I then plotted these values to examine the

Re: [Freesurfer] mri_glmfit skipping .mtx files

Hi Doug, Yes the appear on the 2nd run (including only the missing contrasts). Thanks for that suggestion. Still unsure why they didn't appear with the 1st run though. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete A

[Freesurfer] Insula

Dear FreeSurfers, I was correcting the topology of some subjects, and could not fix some subjects whose insula is misplaced into the temporal lobe / subcortical regions. Inspecting wm.mgz in tkmedit, it seems that there are wm voxels into the hippocampus, perhaps leading surfaces to be built th

Re: [Freesurfer] Freeview.bin - error while loading shared libraries: libvtkverdict.so.5.6 cannot open sharted ...

Hi Zeke, I managed to solve this issue. I have changed the ownership of all folders and files in /usr/local/freesurfer to my Ubuntu user name and now Freeview is working with the sample data. ..Just seeing your email coming in. Best, jk On 06/04/15 22:34, Johannes Kaufhold wrote: > Hi Zeke,

Re: [Freesurfer] Freeview.bin - error while loading shared libraries: libvtkverdict.so.5.6 cannot open sharted ...

Odd. What happens if you type: setenv LD_LIBRARY_PATH /usr/local/freesurfer/lib/vtk/lib/vtk-5.6 Right before typing the 'freeview' command? Does it work then? -Zeke > On Apr 6, 2015, at 5:34 PM, Johannes Kaufhold > wrote: > > Hi Zeke, > > Yes, I'm attempting to open freeview in the same ter

Re: [Freesurfer] Freeview.bin - error while loading shared libraries: libvtkverdict.so.5.6 cannot open sharted ...

Hi Zeke, Yes, I'm attempting to open freeview in the same terminal window in which I have sourced SetUpFreeSurfer.csh. Here's the output from ls -l $FREESURFER_HOME/lib/vtk/lib/vtk-5.6/*libvtkverdict* lrwxrwxrwx 1 root root 22 May 13 2013 /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkv

Re: [Freesurfer] Freeview.bin - error while loading shared libraries: libvtkverdict.so.5.6 cannot open sharted ...

Hello Johannes, You are attempting to open freeview *in the same window* that you sourced SetUpFreeSurfer.csh(sh), correct? Also, can you tell me what the output of the terminal is when you type the following command: ls -l $FREESURFER_HOME/lib/vtk/lib/vtk-5.6/*libvtkverdict* -Zeke On 04/06/2

[Freesurfer] Freeview.bin - error while loading shared libraries: libvtkverdict.so.5.6 cannot open sharted ...

Hi all, I'm super new to Freesurfer. I just set it up on my computer earlier today, following the official wiki on harvard.edu/fswiki... My system: - Ubuntu 14.04 LTS (up to date) - Tcsh installed - Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz

Re: [Freesurfer] mri_watershed Error: indices out of bounds

Hello Edgar, We think we were able to isolate the problem. Version 5.1 is failing to apply the talairach transform to the nu.mgz. It gets computed and applied to the orig.mgz but then not transferred during the next step. When mri_normalize tries to run without this information, it fails, and

[Freesurfer] fs-fast analysis on a group averaged surface

Hi All, I generated a group averaged surface using make_average_surface successfully. Currently, I like to process the fMRI data using this group surface, instead of fsaverage, using the fs-fast pipeline. For doing so, I need to run rawfunc2surf-sess with a parameter where I can input this gr

[Freesurfer] Batch processing

Dear FS experts, I am trying to run recon-all -i plus recon-all -all in a for loop to run trough 250 subjects as efficient as possible. I am using OSX any suggestions from previous cases? Thank you for your help, Pablo