Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

tksurfer overlay scale bar label colors
by Scott Gorlin 03 Mar '08

03 Mar '08

Hi, When I display an overlay scale bar in tksurfer, the labels for the scale bar are displayed in black on a black background. Obviously, this is completely unusable since I cannot read them! They are there, however, because if I move the surface over so that it underlies the scale bar, the text shows up (in black) just fine. Some time ago the text was rendering in blue, which I thought was an odd choice but gave no further thought to it until I noticed the text disappear completely. Now, it seems like a bug to me, but unfortunately I did not notice exactly when the switched occurred. Unless there is some setting buried somewhere to control the text color? I'd love to just set it to white and not deal with this again... I have upgraded both my os and my graphics drivers recently so I wonder if that broke something. The only clue I have is that I know the newest ATI drivers run on AIGLX instead of XGL, could that cause any errors? I'm seeing this in both FS 3 and 4: tksurfer --all-info on my v.4 returns: ProgramName: tksurfer.bin ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2008/03/03-22:12:05-GMT BuildTimeStamp: Sep 17 2007 17:25:01 CVS: $Id: tksurfer.c,v 1.276.2.5 2007/09/16 23:37:27 greve Exp $ User: scott Machine: Renoir Platform: Linux PlatformVersion: 2.6.22-14-generic CompilerName: GCC CompilerVersion: 30200 tksurfer --all-info on my v.3 returns: ProgramName: tksurfer.bin ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 08/03/03-22:14:40-GMT CVS: $Id: tksurfer.c,v 1.183.2.11 2007/01/04 22:30:38 nicks Exp $ User: scott Machine: Renoir Platform: Linux PlatformVersion: 2.6.22-14-generic CompilerName: GCC CompilerVersion: 30200 My system: Ubuntu 7.10 (recently upgraded from 7.04) pentium 4 fglrxinfo returns: display: :0.0 screen: 0 OpenGL vendor string: ATI Technologies Inc. OpenGL renderer string: RADEON X600 Series OpenGL version string: 2.1.7281 Release glxinfo | grep direct returns: direct rendering: Yes xdpyinfo | grep GL returns: ATIFGLEXTENSION ATIFGLRXDRI GLX SGI-GLX Thanks a lot, Scott

1 0

Desikan training sets
by joel bruss 03 Mar '08

03 Mar '08

Is there a place to download the 40 brains used in the creation of the Desikan atlas? If so, would the training data have all of the FreeSurfer data (directories and transform files) so that one could easily create ones own parcellation scheme and create a new brain?

1 0

read_curv
by Reza Rajimehr 03 Mar '08

03 Mar '08

Hi, Using "read_curv", I load the curvature file into Matlab. How can I get the corresponding vertex indices for these curvature values? Thanks, Reza ************************************ Reza Rajimehr, MD Postdoctoral Research Fellow NMR Athinoula A. Martinos Center Department of Radiology Massachusetts General Hospital (MGH) Building 149, 13th Street Charlestown, MA 02129 Phone: 617-669-0930 Email: reza(a)nmr.mgh.harvard.edu ************************************

3 2

Re: [Freesurfer] Editing annotations
by Graham Wideman 01 Mar '08

01 Mar '08

Ronald: There are a couple of articles on this subject on the FS wiki, including one I just posted: https://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_5flabeledit Graham At 2/26/2008 06:55 AM, you wrote: >Forgive me if this has been covered before, but I was unable to find an >answer after searching for a bit. I have been considering editing the final >surface parcellation for those scans that have problems in certain areas. >Can these corrections then be used to correct the surface registration for >the input into Qdec? > >Also, to test out the editing process I have been simply importing the annot >file, editing the labels, then exporting it. Is this the correct thing to >do, and is there a tutorial anywhere about this kind of editing? > >Thanks, > >Ronald Pierson > > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

RE: annotation binary files into ascii format
by Teddy Youn 01 Mar '08

01 Mar '08

Hi everyone, Thanks again for your help from my previous query. I had a question about how to convert the binary format of the annotation file to ascii format, similar to using mris_convert to surface files from binary to ascii. Is there an equivalent program that does the same thing for annotation files? Thanks very much, -Teddy Youn Doris Duke Clinical Research Fellow '07-'08 North Texas TBI Research Center UT Southwestern Medical Center at Dallas Warren Alpert School of Medicine at Brown University, MD '09 Teddy.Youn(a)utsouthwestern.edu (401)-714-2847

3 2

question about moving from freesurfer to afni and keeping registration
by Jena B. Hales 29 Feb '08

29 Feb '08

2 1

Qdec "map label to subjects" error
by nels5614＠umn.edu 29 Feb '08

29 Feb '08

Hello, I have a question in regards to the "map label to subjects" feature in Qdec. Basically, I draw and save a label, and then try to map the label to all of the subjects in my SUBJECTS_DIR, but while running mri_label2label, I get this error: > ERROR: there is a vertex in the label that cannot be matched to the > surface. This usually occurs when the label and surface are from > different subjects or hemispheres or the surface has been changed since > the label was created. Label point 7: vno = 166358, max = 163842 command > failed: mri_label2label --srclabel > /home/bfs-raid1/ryanm/FREESURFER/142_FAE2_blade/v4/freesurfer-from-blade/qdec/lh.parahippocampal_cp --srcsubject fsaverage --trgsubject 18208 --trglabel /home/bfs-raid1/ryanm/FREESURFER/142_FAE2_blade/v4/freesurfer-from-blade/qdec/lh.parahippocampal_cp --regmethod surface --hemi lh I have three groups I am trying to compare, 2 proband groups, and 1 control group. So, I constructed separate .dat files and label files for each- one comparing controls vs. group1, and the other comparing controls vs. group2. I seem to be able to run analyses fine on the data, I am just having problems with the "map label to subjects" feature. The order in my .dat files does differ from the order of datasets in my SUBJECTS_DIR, I don't know if this has anything to do with my error. Any advice/suggestions would be greatly appreciated. Thanks! Miranda Nelson

1 0

RE: [Freesurfer] statistics in aparc.stats
by Pedro Paulo Oliveira Jr 29 Feb '08

29 Feb '08

Aaron, My opinion is that you are right, but maybe the folding index should be taken into account. When we reach a conclusion about this I think is a good question to put in the faq. best regards, Pedro Paulo on E61 -- mens. original -- Assunto: [Freesurfer] statistics in aparc.stats De: "Goldman, Aaron (NIH/NIMH) [C]" <aarong(a)mail.nih.gov> Data: 28/02/2008 22:23 Hi, I just had a question regarding the statistics in ?h.aparc.stats. I'm interested in calculating average thicknesses for several labels combined, and wanted to verify how to do that correctly. The way the stat files are calculated, would it be valid to simply take an average of the listed average thicknesses, weighted by the listed surface areas? Thanks, -Aaron- _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

3 2

help with freesurfer error
by joel bruss 28 Feb '08

28 Feb '08

I was trying to run a single sujbect through recon-all and got the following error: Thu Feb 28 16:34:57 CST 2008 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Thu Feb 28 16:34:58 CST 2008 /fmri/studies/retinotopic/new_retinotopic/3362/3362_resampled.dir/freesurfer_pipeline.dir/sub1/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Linux dendrite 2.6.22.16-0.1-default #1 SMP 2008/01/23 14:28:52 UTC i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Thu Feb 28 16:34:58 CST 2008 I don't speak FreeSurfer and don't understand this error. Please help. -Joel

2 1

qdec error...
by Cameron B. Ellis 28 Feb '08

28 Feb '08

Hi, I pasted an error that I am receiving in qdec below. SUBJECTS_DIR is /space/lightning/2/users/NEAA-freesurfer. If you need any more information from me I will be happy to provide it. Any help is much appreciated. Thanks, troy:cameo[87] ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels ninputs = 48 Checking inputs nframestot = 48 Allocing output Writing to /autofs/space/lightning_002/users/NEAA-freesurfer/qdec/NEA A-freesurfer/y.mgh gdfReadHeader: reading /autofs/space/lightning_002/users/NEAA-freesur fer/qdec/NEAA-freesurfer/qdec.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 txt-untxt 1.01875 Class Means of each Continuous Variable 1 groupPH-gendermale 2.8400 2 groupPL-gendermale 0.5333 3 groupVH-gendermale 0.6000 4 groupVL-gendermale -0.4667 5 groupPH-genderfemale 1.0857 6 groupPL-genderfemale 0.0833 7 groupVH-genderfemale 3.1167 8 groupVL-genderfemale 0.6500 INFO: gd2mtx_method is dods Reading source surface /autofs/space/lightning_002/users/NEAA-freesur fer/fsaverage/surf/lh.white reading group avg surface area 822 cm^2 from file Reading in average area /autofs/space/lightning_002/users/NEAA-freesu rfer/fsaverage/surf/lh.white.avg.area.mgh ERROR: no contrasts specified Error in Analyze: command failed: mri_glmfit --y /autofs/space/lightn ing_002/users/NEAA-freesurfer/qdec/NEAA-freesurfer/y.mgh --fsgd /auto fs/space/lightning_002/users/NEAA-freesurfer/qdec/NEAA-freesurfer/qde c.fsgd --glmdir /autofs/space/lightning_002/users/NEAA-freesurfer/qde c/NEAA-freesurfer --surf fsaverage lh --label /autofs/space/lightning _002/users/NEAA-freesurfer/fsaverage/label/lh.cortex.label

4 4

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