[Freesurfer] Parallel vs. Sequential part

Freesurfer experts, I have been working on openmp parallelization of Freesurfer programs. I'd like to know the ratio of sequential processing parts (which are essentially impossible to be parallelized) to the total amount of processing in order to calculate the theoretical limit of performance im

Re: [Freesurfer] -nobigventricles

Hi Richard this disables some code I wrote a while ago to handle cases with very large ventricles. It didn't work constistently enough to enable it, although it does work significantly better in the upcoming 5.2 (but still should probably be disabled by default). cheers Bruce On Mon, 2 Jul 2

Re: [Freesurfer] regeneration of aseg.mgz following edits

Hi Richard what are you editing? And why would you expect the aseg.mgz to change if you are editing something downstream from it (like the wm.mgz)? cheers Bruce On Mon, 2 Jul 2012, Richard Binney wrote: > Hi Freesurfers, > > I've been trying to understand the implications of various types of

[Freesurfer] regeneration of aseg.mgz following edits

Hi Freesurfers, I've been trying to understand the implications of various types of edits in an attempt to solidify some standardized procedures regarding editing strategies, particularly in severely lesioned (and thus highly vulnerable to RECON failure) brains. In doing so I've been comparing vol

[Freesurfer] -nobigventricles

Out of curiosity, I would like to know what the flag -nobigventricles in the ca_reg and ca_label commands does exactly. Please help. Richard ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/free

[Freesurfer] nearest vertex from talairach coordinates

Hi, I would like to jump to various points on the fsaverage inflated brain in tksurfer based on talairach coordinates reported in a paper. It seems like the easiest way to do this would be to convert the coordinates the closest vertex index, then punch this into the tksurfer gui. A thread

Re: [Freesurfer] error longitudinal processing

Hi Joost, great, but make sure the recon-all processing went OK also. If you had the same directory name twice (for base and for the first time point) stuff will be messed up. Usually recon-all should complain if that happens, but who knows what exactly happened. Best Martin On Mon, 2012-07-02

Re: [Freesurfer] axial sheer

i can fix this if I work with the identity matrix (emacs spm.reg.dat) after automatically coregistering (using spmregister), right? thanks, m From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Borzello, Mia

Re: [Freesurfer] mri_vol2surf and Spherical Surfaces

Hi Doug, Thanks for getting back to me. I'm right around the vicinity of my desired results, but had just three more questions. 1) When running the mri_vol2surf command and specifying --reg, is there any way I can pass in a registration file generated by FSL's flirt command (i.e. flirt -in

Re: [Freesurfer] axial sheer

sure! at the command line: tkregister2 --s BWXX_SurferOutput --mov ct.mgz --reg spm.reg.dat --surf orig this it's a CT of 124 slices from bwh From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve [gr...@n

Re: [Freesurfer] FA (DTI) statistical analysis: 3 covariates

I don't believe that Freesurfer has the tools to use non-imaging data as the dependent variable. The GLM in freesurfer is setup to use the imaging data at the dependent variable. For your question, I'd recommend SAS, STATA, SPSS, or another standard statistical package. Best Regards, Donald McLar

Re: [Freesurfer] request for move through slices

Hi Michael, In freeview you can press Page up/down keys to move through slices. Best, Ruopeng On 7/2/12 5:30 AM, Michael Scheel wrote: > Dear FS experts, > > I am trying out freeview and am extremely fond of it. > I have one feature request. In tkmedit in navigate mode it was possible > moving

Re: [Freesurfer] error longitudinal processing

Hi Martin, changing the dir-names and qdec table to: fsid fsid-base ISI_years Group Gender Age ICV 11298_1 11298_template 0 patient F 16 1441 11298_2 11298_template 1.83 patient F 17.92 1396 solved my problem. -joost On Sun, Jul 1, 2012 at 4:33 PM, j janssen wrote: > Hi Martin, > > thanks

[Freesurfer] request for move through slices

Dear FS experts, I am trying out freeview and am extremely fond of it. I have one feature request. In tkmedit in navigate mode it was possible moving through slices just using the mouse (middle mouse button pressed). Is it possible to implement the same in freeview - it appears that in freeview