Re: [Freesurfer] what does the tk stand for in tksurfer?

Hi Martina, it comes from the tcl/tk code that it interfaces with. cheers Bruce On Thu, 24 Nov 2011, Martina Papmeyer wrote: > Hello, > > I have a very simple question but couldn't find an answer yet. What > does the "tk" actually stand for in tksurfer and tkmedit? > > Many thanks for this info,

Re: [Freesurfer] intensity normalisation and aseg

Hi Mo, that's not a problem. We have different normalizations for different pieces of the recon. For subcortical we use the norm.mgz, which should *not* be eroding borders of thalamus, pallidum, etc The brain*.mgz are for cortex, where we don't care about those borders. cheers Bruce On T

[Freesurfer] what does the tk stand for in tksurfer?

Hello, I have a very simple question but couldn't find an answer yet. What does the "tk" actually stand for in tksurfer and tkmedit? Many thanks for this info, Martina -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___

[Freesurfer] difference between recon-all 4.3 and 5.1

Hi I have two different folders where one is processed by recon-all 4.3 and another by recon-all 5.1. When I compare these two folders I get similar results for fwhm 30 for group difference which is survives fdr, but when I compare results that are do not survived fdr I get very different resu

[Freesurfer] Postdoctoral Fellowship fMRI of Reaching and Grasping

*Postdoc fMRI of Reaching and Grasping, Center for Mind/Brain Sciences, University of Trento, Italy* At the Center for Mind/ Brain Sciences (CIMeC), University of Trento there is soon going to be an opening for a Postdoctoral Fellowship to work with Dr. Angelika Lingnau (http://www.unitn.it/en/c

[Freesurfer] GROUP ANALYSIS ON QDEC

Hi, I've done the recon-all for all my subjects, and everyone ended with no errors. First of all, I don't understand if the recon-all do a volume normalization: why subjects have different number of vertex?if the comparison isnt't vertex by vertex, how is it done? Now I want to do a group Analysis

[Freesurfer] Yeo_JNeurophysiol11_FreeSurfer networks

Dear Freesurfer experts, I would like to use the Yeo_JNeurophysiol11_FreeSurfer parcellations with my dataset and I am not sure what I have to do. I have used the mris_annot_to_segmentation command but I have the following error: mris_annot_to_segmentation BASGU lh inflated ./fsaverage5/label/lh.