Re: [Freesurfer] how is a path created?

2009-01-09 Thread Bruce Fischl
Hi Mike, we've messed with writing such a thing, but never very hard, so no, we don't really have anything. cheers, Bruce On Fri, 9 Jan 2009, Michael Harms wrote: Hello, I was wondering what approach is used to connect marked vertices when using the "Make Path" and "Make Closed Path" tools

Re: [Freesurfer] how is a path created?

2009-01-09 Thread Douglas N Greve
Hi Mike, I can't remember all the details (and the guy who wrote it is gone), but I remember that it was not all that sophisticated (though it works pretty well). I think it choses the next vertex based which one will get it closer in 3D space (and not retrace it's steps). I think it uses what

[Freesurfer] how is a path created?

2009-01-09 Thread Michael Harms
Hello, I was wondering what approach is used to connect marked vertices when using the "Make Path" and "Make Closed Path" tools of tksurfer. Does the "connecting" operation just use the shortest (geodesic) distance between vertices, as determined by the currently displayed surface? Does the 'mri

Re: [Freesurfer] mri_surfcluster problem?

2009-01-09 Thread Lauren LaCount
Looks like it's working again! Thanks for fixing it, Doug, and for pointing out that it was fixed, Pratap! -Lauren On Fri, Jan 9, 2009 at 3:54 PM, Kara Dyckman wrote: > Thanks Pratap, > I'll try it again. > Kara > > Pratap Kunwar wrote: >> >> Kara and Lauren, >> >> I think Doug has fixed this pr

Re: [Freesurfer] mri_surfcluster problem?

2009-01-09 Thread Kara Dyckman
Thanks Pratap, I'll try it again. Kara Pratap Kunwar wrote: Kara and Lauren, I think Doug has fixed this problem. i had similar problem but it is working now. pratap Hi Lauren (and Doug), I'm having the same issue. I ran montecarlo simulations on Friday and then tried to use the re

Re: [Freesurfer] mri_surfcluster problem?

2009-01-09 Thread Pratap Kunwar
Kara and Lauren, I think Doug has fixed this problem. i had similar problem but it is working now. pratap > Hi Lauren (and Doug), >> I'm having the same issue. I ran montecarlo simulations on Friday and >> then >> tried to use the results in mri_surfcluster. It ran, but I also got the >> same

Re: [Freesurfer] Can freesurfer flatten (and dsiplay) certain subcortical areas?

2009-01-09 Thread Koen Van Leemput
We have recently developed a method for automatically segmenting the hippocampal subfields from ultra-high resolution MRI data. The software code is not yet in FreeSurfer, but will be in the future. It produces volumetric segmentations, rather than surface representations, though. - Koen > > C

Re: [Freesurfer] To ask you about mismatch in TR in FSFAST low level analysis

2009-01-09 Thread Douglas N Greve
That actually means that the TR in the file is 175 ms! How was this file created? You can fix it with mri_convert f.nii f.nii --tr 1750 where f.nii is the raw fmri data file doug Francisco Robles wrote: Hi Freesurfer users, My Name is Francisco Robles, from México City, and I am writing

[Freesurfer] To ask you about mismatch in TR in FSFAST low level analysis

2009-01-09 Thread Francisco Robles
Hi Freesurfer users, My Name is Francisco Robles, from México City, and I am writing you to ask you a doubt about the selxavg3-sess process with FS-FAST. The error is the following: it seems like the TR from the analysis is 1.75 (specified in mkanalysis gui) and from data (but i don