Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

what standard are the coordinates from %surfer command line?
by Nguyen, Thang Q 11 Aug '06

11 Aug '06

Hello all, For some reason, when I load a specific analysis surface, the vertex and cursor position freezes on the GUI. Is there any way of determining it from the %surfer command line, i.e. a translation of some sort? % surfer: dmin=0.2796, vno=31207, x=-32.1396, y=-9.1446, z=-16.7376 % surfer: curv=0.000000, fs=0.000000 % surfer: val=0.000000, val2=0.000000 % surfer: amp=0.000000, angle=0.000000 deg (0.000000) % surfer: vertex 31207 marked (curv=0.000000, stat=0.000000) x = (-32.1, -9.1, -16.7), n = (-0.8, 0.2, 0.5). % Unmarking 13794 surfer: vertex 13794 unmarked Thank you for your time, -Thang

1 0

no brain.tri and brain.mgz
by Jiansong Xu 10 Aug '06

10 Aug '06

Dear Friends: I'm playing with the tutorial. I didn't get the brain.tri and brain.mgz files after the first step, see below for the command: recon-all -subjid bert -autorecon1 Best Jiansong

3 2

single button mouse
by Jiansong Xu 10 Aug '06

10 Aug '06

Dear Friend: I'm using Mac OSX with single button mouse. How can I deal with "right click", "middle click", and "left click" Thanks Jiansong

2 1

Copying control points file?
by Jake Freimer 10 Aug '06

10 Aug '06

If I have the same subject on 2 different computers, but I edited the control points on one, can I just copy the tmp/control.dat file over to the other computer and rerun autorecon2-cp, or are there other files it refrences? Thanks -- -Jake

3 2

TKMEdit error on Mac OS 10.4.7
by Kent Ogden 09 Aug '06

09 Aug '06

Hi, I have a brand new Macbook pro with the dual-core intel chip. I downloaded and installed the most recent verision of freesurfer. When I run the configuration script I get source $FREESURFER_HOME/SetUpFreeSurfer.csh -------- freesurfer-Darwin-tiger-stable-pub-v3.0.3 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast SUBJECTS_DIR /Applications/freesurfer/subjects FUNCTIONALS_DIR /Applications/freesurfer/sessions MINC_BIN_DIR /Applications/freesurfer/mni/bin MINC_LIB_DIR /Applications/freesurfer/mni/lib PERL5LIB /Applications/freesurfer/mni/lib/../System/Library/Perl/5.8.6 GSL_DIR /Applications/freesurfer/lib/gsl TCLLIBPATH /Applications/freesurfer/lib/tcltktixblt/lib MISC_LIB /Applications/freesurfer/lib/misc/lib tcsh: gcc: Command not found. tcsh: gcc: Command not found. FSL_DIR /Applications/freesurfer/fsl Which looks ok, except for not finding gcc. tksurfer seems to run fine, but tkmedit just gives an error: Kent% tkmedit bert orig.mgz X Error of failed request: BadRequest (invalid request code or no such operation) Major opcode of failed request: 129 (Apple-DRI) Minor opcode of failed request: 1 () Serial number of failed request: 15 Current serial number in output stream: 15 Can anyone help me with this? Thanks . . . Kent Ogden PhD Associate Professor, Radiology SUNY Upstate Medical University 750 E. Adams Street Syracuse, NY 13210 email: ogdenk(a)upstate.edu voice: (315) 464-5083 fax: (315) 464-5095

4 7

Bad File Descriptor?
by Jake Freimer 08 Aug '06

08 Aug '06

I am guessing that this is a general file error, not something specifically related to freesurfer, but was wondering if anyone had an idea on what might be wrong. 18 vertices at 20 distance writing curvature file /private/Network/Servers/dns2.bmap.ucla.edu/Volumes/BMC3/BMCUsers3/ascott/Documents/freesurfer/subjects/td21new/surf/lh.thickness tee: /private/Network/Servers/dns2.bmap.ucla.edu/Volumes/BMC3/BMCUsers3/ascott/Documents/freesurfer/subjects/td21new/scripts/recon-all.log: Bad file descriptor Darwin lion.bmap.ucla.edu 8.7.0 Darwin Kernel Version 8.7.0: Fri May 26 15:20:53 PDT 2006; root:xnu-792.6.76.obj~1/RELEASE_PPC Power Macintosh powerpc recon-all exited with ERRORS at Tue Aug 8 07:03:55 PDT 2006 Thanks -Jake

1 0

Re: [Freesurfer] Feature request for tkmedit
by d.g.lawyer＠medisin.uio.no 08 Aug '06

08 Aug '06

As Jenni pointed out, tkmedit does ask you to save your edits when you exit using the file menu on the toolbar. I would like to see this feature extended so that it also asks when you close by clicking the x in the corner of the window. You only really need this kind of safety-check when you are tired, which is also the time when you are most likely to close a window by clicking the x in the big window you were just working in, instead of hunting for the file menu on the little tool window on your other monitor. Not that it has ever happened to me, by the way. I just read about it in a book, once.

1 0

Feature request for tkmedit
by d.g.lawyer＠medisin.uio.no 08 Aug '06

08 Aug '06

Hi, It would be great if tkmedit would ask if you have saved your edits before closing. Any chance of getting this added? As it currently stands, it is easy to just press the little x in the corner of the tkmedit window and close it, without recording any of your work. Of course no-one does this when they are fresh, but after hours of editing one sometimes is in a state of rapturous bliss and forgets these little details.

2 1

glutInit bug
by Don.Rojas＠UCHSC.edu 08 Aug '06

08 Aug '06

Dear List: I saw that there was a known issue with glutInit on Debian systems that caused problems with tksurfer. I just thought I'd report that although tksurfer (Freesurfer 3.0.3 stable) runs without error on my two Ubuntu systems (32 bit and 64 bit), I get the same sort of glutInit error message when I try to run scuba: scuba -s 0003 -v T1 Using /usr/local/freesurfer/lib/tcl/tkUtils.tcl Using /usr/local/freesurfer/lib/tcl/histolabel.tcl Using /usr/local/freesurfer/lib/tcl/scuba.tcl freeglut ERROR: Function <glutBitmapCharacter> called without first calling 'glutInit'. Will this issue also be addressed in 3.0.4.? Best, Don

1 0

Freesurfer install error OS Tiger, GSL error
by Charles-Henri Malbert 07 Aug '06

07 Aug '06

Dear collegue, I was using Freesurfer 0.9 and I try to install freesurfer 3. The install went smoothly and I update the cshrc file. The launch of Xterm went fine and the postinstall generate no errors (i.e. the GSL lib was found at GSL_DIR). When trying to test the install using tkmedit bert orig.mgz an error was generated saying that the GSL lib was not found at pubsw (dyld: Library not loaded: /usr/pubsw/packages/ gsl/1.6/lib/libgsl.0.dylib). Indeed no pubsw folder was found at usr. I was using fink and gsl was already installed in sw folder as part of Amide installation (a gnu front end of Xmedcon). May be the problem was arround there? What's the problem Thanks in advance Charles-Henri Malbert DMV, Dr es Sci, HDR Directeur de Recherches UMR SENAH 35590 Saint-Gilles Tel: 02 23 48 50 71 Fax: 02 23 48 50 80

2 1

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