[Freesurfer] Volume (WM Parcellation) of RightCerebralCortex -- Freesurfer 6.0

External Email - Use Caution Dear Freesurfer experts, I am trying to use ADNI MERGE R package to get 'wholebrain' volume. It requires CerebralCortex. The information I get from ADNI merge is "Volume (WM Parcellation) of RightCerebralCortex". But when I ran Freesurfer reconall 6

[Freesurfer] HBT hippocampal segmentation

External Email - Use Caution Hello, I was just asked by a reviewer how the head body and tail of the Freesurfer subfield segmentation is determined. I know that there is no differentiation of the tail, however, there are differentiations between the head and body of the different

[Freesurfer] Freesurfer analyses in MATLAB

External Email - Use Caution Hi I'm interested in running some analyses in matlab using freesurfer commands. I'm running an interaction effect, however I'm having issues residualizing the brain values to plot. For running interaction effects I'm running it by inputting: X=load('X

[Freesurfer] Custom location of license file

External Email - Use Caution Hi, We’d like to install FreeSurfer globally for our users on a CentOS HPC system. Is it possible to define an alternative location for the FreeSurfer license file, e.g. ~/.license, so that users can use their individual license files with the glo

[Freesurfer] Multiple comparisons

External Email - Use Caution I would like to know how the correction is made for multiple comparisons in the statistical analysis? We are using QDEC, with False Discovery Rate or Montecarlo Null-Z. Is there a better way to do that? Best, JC.

Re: [Freesurfer] 4D multi-frame parcellation

External Email - Use Caution Oops sorry for the mistakenly reply. I will pay more attention in the future. Bert is the folder with the anatomical data. I tried the following steps with the 4D volume but failed. Then I checked the registration result after bbregister and found that

[Freesurfer] Fw: surface group analysis with qdec

External Email - Use Caution Hi, I'm trying to run a surface based group analysis comparing patients and HC, correcting for disease duration. I enclose here the fsgd file and the design matrix. I've followed all the steps of the tutorial (http://surfer.nmr.mgh.harvard.edu/fswiki

Re: [Freesurfer] Spatial smoothing for cortical folding measures

Hi Yang the size of the smoothing kernel depends on the size of the effect you are looking for (this is called the matched filter theorem), so there is no general smoothing size that is appropriate. We smooth a bit by default for visualization purposes, but you can pick any smoothing size you