Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

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. > > >

1 0

White matter surface edits
by Martin Ystad 24 Nov '08

24 Nov '08

Hi, I have been trying to make freesurfer include all of my white matter in the wm-surface. It seems to run directly across some of the gyri in my brain volume (see attached picture). I first tried to add control points at the base of the gyri, and then along the gyri, but that did not seem to have much effect. Then I manually drew the white matter onto the wm.mgz-volume (see attached picture), but that did only help for some of my gyri. Do you have any tips on how to force freesurfer to include the remaining white matter in the wm surface? Thanks, Martin Ystad

2 1

stats in freesurfer
by Lúcia Garrido 24 Nov '08

24 Nov '08

Dear all, I have a few questions about stats in freesurfer that I'd be very grateful if you could answer. 1. Is it possible to reduce the search from the whole brain to a smaller region of interest to apply corrections for multiple comparisons? For example, if I'm interested in differences in the fusiform gyrus, can I restrict the FDR correction to the fusiform? 2. Is it important to control for any global measure when comparing cortical thickness? For example when comparing grey matter volume, it's good practice to control for the intracranial volume. In case of cortical thickness (and other dependent measures in freesurfer), do you know how these are affected by the intracranial volume (or other measures) and how these could be controlled? 3. Finally, I posted a question a few days ago about comparing volume using freesurfer. I'm sorry for insisting on this but I still haven't found any response. My question was whether it's possible to compare volume maps in freesurfer. I'm using an older version (4.0.4) and my impression is that the most recent version might have this feature, but this is unclear to me. I'd be very grateful if you could let me know if this is the case. And if there's any way in which I can compare volumes usig data pre-processed using the version I have. Thank you very much! Best wishes, Lucia

2 2

Hi, a problem!
by Zhangyuanchao 23 Nov '08

23 Nov '08

Using lgi, I want to know whether I should mask out the corpus callosum and the structures which lies below the corpus callosum as I do it using thickness measure. Thanks! ___________________________________________________________ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/

2 1

mri_ca_train: CGAupdateNodeCovariance
by Jason S. Minamora 23 Nov '08

23 Nov '08

I got the following output after running the second stage of `rebuild_gca_atlas.csh', which starts by training on all segmented subjects. The first stage (which performs a Tal reg on the first subject listed in env var $SUBJECTS) finished without problems: echo "$train using all subjects, using ${M3D_ONE}, producing ${GCA}..." set cmd=($train -prior_spacing 2 -node_spacing 4 -mask ${MASK_VOL}) set cmd=($cmd -parc_dir ${SEG_VOL} -xform ${M3D_ONE} -T1 ${T1_VOL} -check) set cmd=($cmd ${SUBJECTS} ${GCA}) --------- Execution stopped after this step: --------- (STDOUT) computing covariances for subject A59, 1 of 4... reading volume /Users/jsm/work/subjects/A59/mri/brain.mgz for masking... gunzip -c /Users/jsm/work/subjects/A59/mri/transforms/talairach_one.m3z GCAupdateNodeCovariance(10, 35, 23, 4): could not find label --------- Here `$SUBJECTS' was set to 'A59 A62 f18 f20', with "A59" being the first subject. Thanks in advance, Jason

3 6

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer