[Freesurfer] fsaverage problem

Hello Bruce, thank you for your reply, and sorry that i couldn't reply on your mail (i don't know how). What do you mean by mapping an image to fsaverage space? do you mean we get a matrix of transformation? and if yes do we have access to this matrix? or do mean that when a subject is added the f

[Freesurfer] Subcortical Segmentation Information

Hello, I am writing to see if there is more detailed information available about the protocols for identifying the caudate, putamen, and thalamus in the automated subcortical segmentations. I have read the Fischl et al. (2002) paper and I understand the general methodology described there; but

[Freesurfer] Setting the number of Open MPI Threads in mri_em_register

Hi all, I'm running the FreeSurferPipeline script in the Human Connectome Project Pipelines. My network administrator doesn't want me running multi-threaded scripts, so I'm trying to remove the use of Open MPI from this script (or set the number of threads to 1). I noticed the script includes th

Re: [Freesurfer] Default FA threshold value for TRACULA

Hi - Tracula does not use tensors for tractography, so there is no FA threshold applied to reconstruct the tracts. On Wed, 3 Jun 2015, Woo-Suk Tae wrote: Dear TRACULA expertsIs there any FA threshold value for TRACULA? If yes, what is the FA cutting value and how can I change it?  Woo-Suk,

Re: [Freesurfer] Timecourses In freesurfer

what are you trying to do exactly? And why are you using an ancient version of FSFAST? doug On 06/02/2015 03:37 PM, Jonathan Oron wrote: > Hi All, > I’ve been trying to get time course data in tksurfer > I’ve used selxavg2 to create bfloat mgh and nii.gz files and yet I can’t load > these into t

Re: [Freesurfer] GLM analysis on CBF maps

Continue with what you have done, do not model it as a continuous variable. doug On 06/02/2015 04:03 PM, Matthieu Vanhoutte wrote: > Dear Experts, > > I have run GLM group analyses with Freesurfer tools according DODS > model, with six classes ((Male,Female) ; (Control,Left,Right)) and one > age

Re: [Freesurfer] Release of FS version 6.0

sure. Sorry for the rant. We are meeting today to see where we are at with V6 and are still hoping to get it out "soon" whatever that means :) Bruce On Wed, 3 Jun 2015, Jürgen Hänggi wrote: Dear Bruce thanks for the information Cheers Jürgen --

[Freesurfer] The colorwheel of rtview

Dear Freesurfer experts, I posted my question before, but didn't get any answer. I really hope to get the answer! I did the retinotopy analysis with the guide of freesurfer and viewed the results by rtview. How could I get the colorwheel with which I can define the visual area? I also really want