[Freesurfer] possible to enable openmp with tracula cvsreg?

Hi, I noticed in the output for tracula -prep I am currently running using cvsreg it mentions openmp=1, I was wondering if there is a way to enable more than 1 core for openmp for tracula-prep? Thanks, -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laborato

[Freesurfer] tracula cvs_reg taking greater than 24 hours

Hi, I am running tracula prep step using doregcvs=1, and the case has been processing for greater than 1.5 days now. To get it to run, I had to follow the instructions from here: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg36133.html Any suggestions if I am doing something wron

Re: [Freesurfer] Freesurfer gifti-Surface in Matlab

Bastion, Hi, I'm a bit late in this reply. You can use 'mris_info lh.white.gii' to display the matrices in that file. The one labeled 'FS_VOLGEOM_RAS' is the one that will register the surface with the orig.mgz volume file. Note that it will always be three numbers (c_r, c_a, c_s) which just shi

[Freesurfer] Vertex analysis cluster values

Hi Freesurfer users, I ran a GLM vertex analysis testing an interaction between group and a task measure, and a few clusters popped up that survived correction. I extracted the mean thickness values at the clusters (using cache.th13.abs.y.ocn.dat) in order to plot these interactions in graph form.

Re: [Freesurfer] Seg fault

Hi, So I've now tried several subjects on my own computer and they all gave me this fault. I then tried several on another and it worked. If I didn't update my OS version or my freesurfer version, is there another software update that could give me this fault? Many thanks, Gill On May 30, 201

Re: [Freesurfer] How to deal with a skewed T1 image

Not necessarily. Check the surfaces and aseg, but it might be fine Bruce > On Jun 6, 2014, at 12:05 PM, Vy Dinh wrote: > > Dear Freeesurfer community, > > I've attached a coronal view of a T1 image in tkmedit that is slightly > oriented away from the center. The subject has been processed thr

Re: [Freesurfer] Vol stats of precentral gyrus

Hi Hugh I don't think any of it is used to generate subcortical volume stats. Why would it be? cheers Bruce On Fri, 6 Jun 2014, Hugh Pemberton wrote: > Hi everyone, > I was wondering if someone could comment on which portion of the precentral > gyrus is used to > produce subcortical volume stat

Re: [Freesurfer] Quality control of the splitting of midline structures?

would automatically generating a medial snapshot with the aparc overlaid suffice? On Fri, 6 Jun 2014, Jensen, Sarah wrote: Dear Freesurfers,   I have a question about whether it is possible to check how well each participant in my study lines up with the Freesurfer template in order to chec

[Freesurfer] Quality control of the splitting of midline structures?

Dear Freesurfers, I have a question about whether it is possible to check how well each participant in my study lines up with the Freesurfer template in order to check how midline structures were split. I am concerned about how well my ACC ROIs line up with the midline of the brain, and would

Re: [Freesurfer] Vol stats of precentral gyrus

Hi everyone, I was wondering if someone could comment on which portion of the precentral gyrus is used to produce subcortical volume stats? Is it just medial or lateral the whole gyrus? Many thanks and all the best, Hugh On 5 June 2014 12:25, Hugh Pemberton wrote: > Hi everyone, > > I was won