Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30064 discussions

fsl
by Jiansong Xu 13 Aug '06

13 Aug '06

Dear Friends: My fsl was installed in the directory /usr/local/fsl. I can use fsl before download freesurfer, but I cannot open fsl any more after installed FreeSurfer. Any suggestions? Thanks Jiansong

2 1

surface coordinate
by Anqi Qiu 11 Aug '06

11 Aug '06

Hi, Can someone tell me how to transform the surface data back to have the same coordinates as the volume? Not centering it so I can superimpose the surface in the image volume. Thanks! Anqi Qiu Center for Imaging Science The Johns Hopkins University

1 0

error message at SkullLTA
by Chacko Cherian 11 Aug '06

11 Aug '06

Hello all, I got this error message while running one of my subjects. i checked the /mri directory but nu_noneck.mgz was not created instead nu.mgz was there. THanks in advance. Chacko Cherian. Arizona State University. reading labels out of gcam file... removing structures at least 25 mm from brain... 12620067 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 18 minutes and 46 seconds. #-------------------------------------- #@# SkullLTA Wed Aug 9 08:35:57 MST 2006 mri_em_register -skull -t transforms/talairach.lta nu_noneck. mgz /ud/chacko/freesurfer/average/RB_all_withskull_2006-02-15. gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacin g = 5 using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach_with_skull.log reading '/ud/chacko/freesurfer/average/RB_all_withskull_2006-02-15.gca'... setting gca type = Normal gca type average std = 23.5 using min determinant for regularization= 55.2 0 singular and 6473 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... zcat: /ud/chacko/freesurfer/subjects/AD_norm_cor25all111/maketemp/norm/subj21/mri/nu_noneck.mgz.gz: No such file or directory mghRead(/ud/chacko/freesurfer/subjects/AD_norm_cor25all111/maketemp/norm/subj21/mri/nu_noneck.mgz, -1): read error mri_em_register: could not open input volume nu_noneck.mgz. Linux ernie 2.6.17.1 #4 PREEMPT Sat Aug 5 09:35:33 MST 2006 i686 pentium4 i386 GNU/Linux recon-all exited with ERRORS at Wed Aug 9 08:36:35 MST 2006

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point correspondence of ?h.sphere.reg
by wanlin 11 Aug '06

11 Aug '06

Hello all: After processing cortex reconstruction using Freesurfer, i find that the number of vertices of ?h.sphere.reg for different people is different, How to make sure the point correspondence? the tutorial said that the ?h.sphere.reg file is the results of alignment between subjects and the standard template. If I want to perform hypothesis test for some features on every vertex, How should i do? thanks wanlin

3 2

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

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