[Freesurfer] problems with loading a pial surface

Hello Freesurfers I still have the problem using a tcl script that should load the pial surface on a patch in tksurfer. I tried to use the following three commands: 1. set gaLinkedVars(vertexset) 3 SendLinkedVarGroup view redraw 2. read_pial_vertex_coordinates redraw 3. read

Re: [Freesurfer] incorrect GM/WM surfaces

what may have gone wrong. >> See attached screenshot from tkmedit. >> Any suggestions how to fix this would be helpful. >> >> I have processed other datasets collected from the same scanner using the >> same sequence which seem to have correctly identified the pial and >>

Re: [Freesurfer] problems with loading a pial surface

Hi Iris, updating. I would try: set_current_vertex_set 3 UpdateLinkedVarGroup view UpdateAndRedraw if this doesn't work, tell us, and if you don't get a response in the next day or so, can you repost in a week? We are flat out trying to prepare for our upcoming course and also get 5.1 out th

[Freesurfer] preproc-sess OSX bug fix getrunlist

Hello, I am running into an issue with running preproc-sess on OSX as outlined here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15896.html I saw Doug posted a bug fix that should solve this problem, however, I am unable to access it from: ftp://surfer.nmr.mgh.harvard.edu/transf

[Freesurfer] MRI analyst position

YORK UNIVERSITY Job Type: Contract Location: Toronto, ON, CANADA; Industry: Education Company URL: http://www.yorku.ca Date Posted: March 31, 2011 JOB TITLE: MRI Analyst, Neuroimaging Laboratory TYPE OF POSITION: Contract – 1 year contract with a possibility of renewal SALARY: $60,000 - $75,00

[Freesurfer] Distance between two points along cortical

Hello FS Experts, Suppose we have two points on the cortical surface (pial for example), we want to know the distance between these two point along cortical surface (not direct distance). Does FS report this kind of distance? Any suggestion will be very appreciated. Aize

Re: [Freesurfer] Where can I find long_mris_slopes

Hi Lan, this tool will be available in 5.1 Martin On Wed, 2011-03-30 at 11:03 -0700, lan lin wrote: > I installed freesurfer 5.0 and want to use long_mris_slopes to prepare > the longitudinal data but couldn't find the command. Where can I find > it? > > thanks > Lan >

Re: [Freesurfer] Distance between two points along cortical

This question comes up sometimes -- and the short answer is 'yes', there is a tool that can allow you to do this. Although it will be available in the next version of FS (5.1), it is still a bit rough around the edges. It is called 'mris_pmake' and to use it to determine the distance between two po

Re: [Freesurfer] Fwd: bbregister bug? with init-spm option--flips left and right

Thanks, Doug and Michael--that did the trick! What is the status of this issue for newer versions of FreeSurfer (e.g., 5.0)? Tyler On Tue, Mar 29, 2011 at 8:17 AM, Douglas Greve wrote: > > As Michael says, with spm8 you have to use nifti. When 4.5 was written, > spm8 was not around (or not used

Re: [Freesurfer] Distance between two points along cortical

It is very good to know FS has this function. It will be very helpful for us. Thanks. Aize > Date: Fri, 1 Apr 2011 13:57:23 -0400 > From: rudo...@nmr.mgh.harvard.edu > To: caoa...@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Distance between two points along c

[Freesurfer] resampling vol to surface

Hi guys, i am using the freesurfer-fsl integration to use labels from the freesurfer cortical surface as seeds for probtrackx probabilistic diffusion tractography. when the output of probtrackx is generated it is already in the freesurfer conformed space. I want to resample the output of probtr

Re: [Freesurfer] Distance between two points along cortical

Hi Aize, great circles on the ?h.sphere should be within about 15% of the true geodesic distance. We routinely use them to estimate distances. cheers Bruce On Sat, 2 Apr 2011, caoaize wrote: > > > Hello FS Experts, > > Suppose we have two points on the cortical surface (pial for example), we >

Re: [Freesurfer] add subject to group but cannot find brain for 049

Hi Knut does the file brain.mgz exist in $SUBJECTS_DIR/004/mri? If so, can you run ls -l $SUBJECTS_DIR/004/mri/brain.mgz Bruce On Thu, 31 Mar 2011, Knut J Bjuland wrote: > i used the following command to repeat a failure output. i used just one > subject to get a fast output since my pc is

[Freesurfer] Vertex-by-vertex analyses within ROIS?

Hello Freesurfers, I am happy to find out that it is possible to carry out vertex-by-vertex analyses for specific ROIs. Can someone help me understand, 1. How to run such a vertex-by-vertex analyses for certain ROI or ROIs? 2. Can we apply cluster-wise correction or FDR to the ROI to correc

[Freesurfer] creating labels in tksurfer

Hi there, I'm having difficulty creating labels in tksurfer (v4.5). I followed the "Creating Labels" instructions on the Wiki, however clicking Fill on the closed path didn't seem to do anything. I used save label anyway, and tried to load this new label again, and even though it says "7681 nonze

Re: [Freesurfer] creating labels in tksurfer

Hi Ilana, usually a bizarre labeling means the annot is out of date. Try running recon-all with -make all on that subject and see if it needs to recreate anything. Not sure what's up with your label, but things can act strangely when the surfaces are out of date cheers Bruce On Fri, 1 Apr 201