Freesurfer November 2008

freesurfer@nmr.mgh.harvard.edu

70 participants
98 discussions

shell choice
by Jared Price 28 Nov '08

28 Nov '08

Hello freesurfer gurus, I noticed on the wiki that they recommend using tcsh when running freesurfer, although they say other shells can be used. Is there a significant advantage to using tcsh when running freesurfer? If I would rather use bash is there any significant reason not to? Warmest regards, -Jared

4 3

tksurfer doesn't work
by RafaelHuber＠access.unizh.ch 28 Nov '08

28 Nov '08

Dear Freesurfer Experts I have a Macbook 2GHz Intel Core 2 Duo (MAC OSX Version 10.4.11) and just installed Freesurfer v4.1.0. I followed the installation and setup steps of the freesurfer homepage and everything seemed to work well. When I finally tried the "tksurfer bert rh pial" command I got an error message called: "GLUT: Fatal Error in tksurfer.bin: could not open display: ". Later on I saw, that tksurfer actually works, but only when I type the command into the X11 terminal. Is this correct? Do I always have to work with the X11 terminal, or did I do something wrong? Thanks for your help in advance! Cheers, Rafael Huber

2 1

problem with intensity normalization and mri banding artifacts
by David Qixiang Chen 27 Nov '08

27 Nov '08

Hi all, I'm running into a problem where some of my scans have varied brightness between slices. What happens is that this results in heavy banding of the resulting scans, and this creates major problem for freesurfer to segment out wm because of the variation in signal intensity. Intensity normalization doesn't seem to correct this kind of signal problems. I'm wondering what would be a good way to go about correcting this? I'm been doing control points and wm edits, but because the wm intensity is not standarized across the slices, I think it's just an exercise in futility so far. I've attached a screen shot. Thanks! - David Qixiang Chen

2 3

convert .img to .mgz
by Luke Tseng 27 Nov '08

27 Nov '08

how do i convert a .img file to something i can view in freesurfer like .mgz? mri_convert?

2 1

qdec error
by Prapti Gautam 26 Nov '08

26 Nov '08

Hi, I’ve run across the following error while trying to run qdec in my linux 64 bit computer, qdec.bin: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory Is there any specific file that I need to download or change configuration of? I apologise if this has been covered before in the mailing list, Any help is greatly appreciated, Thanks, Prapti

3 2

Qdec error message
by Julia Altenburg 26 Nov '08

26 Nov '08

Hey all. I got the same error message as Jenifer and Dorit described earlier. [lips-computer-2:~/Desktop/freesurfer_Julia] Preissle% qdec ERROR: In /usr/pubsw/packages/vtk/5.0.4/src/VTK/Rendering/vtkXOpenGLRenderWindow.cxx, line 219 vtkXOpenGLRenderWindow (0x4921ff0): Could not find a decent visual I get the message three times, but it's possible to open the qdec table after that. I've attached a screenshot of what the Display looks like. Is there anything I can do to solve this problem? I've tried the advices you've given previously, but the message ist still shown. I'm working with FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-tiger-i686-stable-pub-v4.0.5 Kernel info: Darwin 8.11.1 i386 Thanks in advance Cheers Julia

2 1

Hi, a question on lgi
by Zhangyuanchao 26 Nov '08

26 Nov '08

Dear Mr or Ms, If a subject was identified with severe polymicrogyria, which is a brain malformation marked by development of numerous microgyri, what will the lgi of the subject behave? I want to know whether the lgi of the subject would increase or decrease compared with that of the brain of a normal subject. And why? Could you tell me the reason basing on the calculation method of lgi? Thanks. ___________________________________________________________ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/

2 1

fs-fast smoothing
by Scott Gorlin 25 Nov '08

25 Nov '08

Hi, I'd like some clarification on the recommended procedure for smoothing functional data across the cortical surface in FS-FAST. I've managed to get it working using the following procedure: 1) analyze my data using selxavg3-sess in the native space, without smoothing 2) resample the averages into the spherical space using func2sph-sess 3) smooth these averages using sphsmooth-sess (which required several edits to work with .nii files) 4) recreate the contrasts in the smoothed sph space with stxgrinder-sess 5) paint the analysis onto the surface with paint-sess (which also required edits for .niis) 6) view with surf-sess (which I had to edit to read the subject properly) Surely there's a simpler way to accomplish this? I'm particularly confused because the online documentation says that selxavg3 replaces stxgrinder, but it seems stxgrinder has to be called to make contrasts in non-native space (and uses different code to produce the contrasts than selxavg). Plus, the revision date for stxgrinder is more recent! Then, it seems odd that isxconcat will reproject the data for a group analysis if it's already sampled on the surface via func2sph. Thanks, Scott

4 6

Volume Statistics
by Alexa Nardelli 25 Nov '08

25 Nov '08

Hi, I have performed subcorticol segmentation using freesurfer and I am now interested in looking at the volume of the hippocampus and the amygdala; the volume statistics under aseg.stats and those under wmparc.stats are different. Is this normal and if so, which ones should I be using? Thanks Alexa

6 9

colormap
by Siddharth Srivastava 24 Nov '08

24 Nov '08

-with relevant subject-- sorry for multiple sends. On Mon, Nov 24, 2008 at 8:43 PM, Siddharth Srivastava <siddys(a)gmail.com>wrote: > Hi everyone, > Any recommendations on how to set up a proper colorscale > for > visualization? My data do not have negative values (lgi, but a large range, > 1 - 15, and i would like to > use the entire range of blue-green etc. maps. I have been playing around > with > the color-scale window in the configure section, but have not managed to > get > anything sensible as yet. What would you suggest? > thanks, > sid. > > >

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Freesurfer November 2008