Re: [Freesurfer] symmetric template in freesurfer

Thank you very much, Doug. Will study. Cheers, Xi-Nian. On Mon, Oct 7, 2013 at 11:22 AM, Douglas Greve wrote: > > Yes, it is released. See https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi > doug > > ps. Please remember to post to the list. Thanks! > > > > > On 10/6

[Freesurfer] Usage of --area option in estimating the vertex-wise maps of surface area

Hello Doug, I am doing some association studies between functional measures and surface area. In using mris_preproc, there is an option --area. Does this do sth similar to that as Winkler et al. (2012)? Winkler et al., 2012. Measureing and comparing brain cortical surfacearea and other areal qua

[Freesurfer] Measures on Overall Registration Quality in Freesurfer

Dear FS Developers, Is there any metrics output by Freesurfer for measuring the overall quality or error of the surface registration from an individual brain to the fsaverage brain? I mean something like the bbregister.dof6.dat.mincost given by bbregister. Many thanks! -- Xi-Nian Zuo, Ph.D of App

Re: [Freesurfer] Measures on Overall Registration Quality in Freesurfer

Thanks very much, Bruce :) On Sun, Nov 18, 2012 at 9:17 AM, Bruce Fischl wrote: > If you look in the recon-all.log it should give the final error functional > value from mris_register > > cheers > Bruce > > > > On Sun, 18 Nov 2012, Xinian Zuo wrote: > >> Dear

[Freesurfer] FreeView Gave Errors

Freesurfers, Anyone saw some errors below from FreeView? -error message-- freeview.bin: tnl/t_vertex.c:407: update_input_ptrs: Assertion `a[j].inputstride == vptr->stride' failed. --

Re: [Freesurfer] FreeView Gave Errors

in the interface? > > cheers > Bruce > > > > > On Thu, 8 Dec 2011, Xinian Zuo wrote: > >> Freesurfers, >> >> Anyone saw some errors below from FreeView? >> -error >> message

[Freesurfer] Cluster-wise correction for multiple comparisons: customized Zstats data

Hi List, I have a question on how to write out the matlab vector containing the Z-statistics and perform subsequent multiple corrections. I already read some functions and know how to write it to a mgh surface file. Here, my question is 'is there any specific things on the header of the surface fil

Re: [Freesurfer] Cluster-wise correction for multiple comparisons: customized Zstats data

SD files are > located here $FREESURFER_HOME/average/mult-comp-cor > doug > > > Xinian Zuo wrote: >> >> Hi List, I have a question on how to write out the matlab vector >> containing the Z-statistics and perform subsequent multiple >> corrections. I already read

[Freesurfer] Co-registration in FS

whatever other commands) to take skull-stripped highres for the co-registration (in fact, the brainmask.mgz already there)? Or I was wrong, reg_feat2anat did this consideration? Any suggestions would be appreciated! -- Xinian Zuo, Ph.D Associate Research Scientist Institute for Pediatric Neuroscience

[Freesurfer] error on reconall2 stage

Hi, FSers I performed auto-reconall script and faced an error in below command, mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance bao-xin Segmentation fault Anyone can give me suggestions how to look for further

[Freesurfer] Command line to map volume data to surface data

without launching the tksurfer gui? I found there is a command mri_vol2surf, but not sure about these default settings in tksurfer gui. Really appreciate it if some know and like to give your suggestions. -- Xinian Zuo, Ph.D Associate Research Scientist Institute for Pediatric Neuroscience NYU Child

Re: [Freesurfer] Command line to map volume data to surface data

mri_vol2surf --help > > I think tksurfer uses a projfrac of 0 and nearest neighbor interpolation. > You can load the result directly into tksurfer to see if it looks the same. > > doug > > > Xinian Zuo wrote: >> >> Dear surfers, >> >> Hi, I used freeesurfe

Re: [Freesurfer] Command line to map volume data to surface data

#x27; in the command. What is the relationship between the two? xinian On Thu, Aug 5, 2010 at 2:13 PM, Douglas N Greve wrote: > I'm not entirely sure how tksurfer is sampling from the volume to the > surface. mri_vol2surf is the gold standard, so use that. > > doug > > Xi

Re: [Freesurfer] Command line to map volume data to surface data

mooth. See the --help. > > doug > > On 8/5/10 5:34 PM, Xinian Zuo wrote: >> >> Nice to know the gold standard, now going with the mri_vol2surf :) >> One more question: As for the overlay surface smoothing option, in >> tksurfer gui, I can set it by following '

[Freesurfer] IA64 release?

Hi, fsurfer team, I am just asking if there is any coming release of fs5.0 for ia64 cpu architecture? Thank you! Best, -- Xinian Zuo, Ph.D Associate Research Scientist Institute for Pediatric Neuroscience NYU Child Study Center 215 Lexington Ave., 14th Floor New York, NY 10016 Phone: (212) 263

Re: [Freesurfer] IA64 release?

ase anytime soon.  we do > not have itanium machines locally (the prior build made use of an > account at SDSC's computing center, and they retired their ia64 cluster > last year). > > n. > > On Fri, 2010-08-20 at 16:24 -0400, Xinian Zuo wrote: >> Hi, fsurfer team, >

[Freesurfer] zero intensities within brainmask.mgz

Hi, FSers, Sorry for sending again. I am using FS5. 0 to extract brain mask for other analyses. I found there were always some zero intensities within voxels of some CSF, thus lead to a brain mask with some small holes inside after binary operation. Is there a way of filling them? Thanks! -- Xi-N

[Freesurfer] Opening positions

Opening positions (postdoc, research assistant, or professorship) for collaborative projects from the Center for Human Brain Research, Hangzhou Normal University (Professor WENG Xuchu, wen...@psych.ac.cn), Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University (Professor Z

[Freesurfer] FS5.1 for CentOS4 works for CentOS5-like OS?

Dear FS team, Only see new 5.1 version for CentOS4 in the website. Thanks, XN. -- Xi-Nian Zuo, Ph.D of Applied Mathematics (http://lfcd.psych.ac.cn) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/list

[Freesurfer] How to refine the recon-all results from old version?

Hi, FSers We have lots of data run based on a previous version (see 5.0). Is there any way to refine them using the FS5.1 pipeline but not to re-run all steps of recon-all? Many thanks! -- Xi-Nian Zuo, Ph.D of Applied Mathematics (http://lfcd.psych.ac.cn)

Re: [Freesurfer] How to refine the recon-all results from old version?

Thanks, Bruce! On Fri, Jun 3, 2011 at 8:18 PM, Bruce Fischl wrote: > HI Xi-Nian > > no, sorry, you need to rerun them, although you shouldn't need to do any > manual intervention. > > cheers > Bruce > > > On Fri, 3 Jun 2011, Xinian Zuo wrote: > >> Hi