Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

Sulcal depth and width
by Kelly Silva 01 Apr '09

01 Apr '09

Hello, How can I calculate the sulcal depth and the sulcal width for each hemisphere and for specific ROIs? Thanks and regards, Kelly Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

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grey/white matter volumes of cortical ROIs
by Jose Luis Cantero Lorente 01 Apr '09

01 Apr '09

Hi, I would like to obtain gray matter volume (not thickness) values for several new cortical ROIs that I have created with tkmedit, but to my knowledge this is not straight-forward with Freesurfer. We have tried this option: mris_anatomical_stats -l ?h.name.label <subject > Is that correct for my purpose? Could anybody tell me if there is another more correct way to aim this goal by using Freesurfer? How can I get the white matter volume values for the same ROIs? Any help would be very welcome. Best, Jose --- Jose Luis Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cellular Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor(a)upo.es http://www.upo.es/neuroaging/es/

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Re: [Freesurfer] tksurfer error
by Pedro Paulo de Magalhães Oliveira Junior 01 Apr '09

01 Apr '09

It seems that you are using running this Centos inside a VMWare. TkSurfer works fine in Virtualbox (2.1.4) but I'm not sure it'll do in current vmware ----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.netfilter.com.br 2009/4/1 Elisa Dell'Oglio <delloglio(a)bwh.harvard.edu> > Attached is the output of dmesg. I am not very familiar with evaluating the > output of glxgear. Here is a sample of the frames per second that is > printing: > > 7920 frames in 5.0 seconds = 1569.891 FPS > 8280 frames in 5.0 seconds = 1654.312 FPS > 7920 frames in 5.0 seconds = 1576.902 FPS > 8520 frames in 5.0 seconds = 1688.239 FPS > 9000 frames in 5.0 seconds = 1789.300 FPS > 8520 frames in 5.1 seconds = 1683.927 FPS > 8359 frames in 5.1 seconds = 1650.856 FPS > 8280 frames in 5.0 seconds = 1653.440 FPS > 8280 frames in 5.0 seconds = 1643.529 FPS > 8040 frames in 5.0 seconds = 1599.484 FPS > 9227 frames in 5.1 seconds = 1825.203 FPS > 8760 frames in 5.1 seconds = 1732.738 FPS > 8160 frames in 5.0 seconds = 1630.169 FPS > 8400 frames in 5.0 seconds = 1677.716 FPS > 8520 frames in 5.0 seconds = 1701.086 FPS > 8021 frames in 5.1 seconds = 1587.792 FPS > > thanks, > > Elisa > > > 2009/4/1 Pedro Paulo de Magalhães Oliveira Junior <ppj(a)netfilter.com.br> > >> Try running glxgears >> >> Can you post the output of *dmesg *command >> >> >> >> 2009/4/1 Elisa Dell'Oglio <delloglio(a)bwh.harvard.edu> >> >> Thanks you. I actually tried this already (I saw this solution was >>> suggested to users that experienced the same problem). Unfortunately this is >>> not working, I still get the error message: >>> surfer: ### redraw failed: no gl window open >>> >>> Is there anything else that you would suggest to try? >>> >>> Thank you in advance, >>> Elisa >>> >>> 2009/4/1 Pedro Paulo de Magalhães Oliveira Junior <ppj(a)netfilter.com.br> >>> >>> If you are using tcsh >>>> >>>> setenv doublebufferflag 1 >>>> >>>> in bash >>>> >>>> export doublebufferflag=1 >>>> >>>> ----------------------------------------------------------- >>>> Pedro Paulo de M. Oliveira Junior >>>> Diretor de Operações >>>> Netfilter & SpeedComm Telecom >>>> --- Novo Netfilter 3.0 www.netfilter.com.br >>>> >>>> >>>> >>>> On Wed, Apr 1, 2009 at 12:07, Elisa Dell'Oglio < >>>> delloglio(a)bwh.harvard.edu> wrote: >>>> >>>>> Hi all, >>>>> >>>>> I am running freesurfer on CentOS (5.2-x86_64). I get the folowing >>>>> error when I launch tksurfer: >>>>> surfer: ### redraw failed: no gl window open. >>>>> The result is that no surface is shown. >>>>> >>>>> Any advice on how to solve the problem? >>>>> >>>>> Thanks, >>>>> Elisa >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>> >>>> >>> >>> >>> -- >>> Elisa Dell'Oglio, MS >>> Research Associate to Dr. Bakshi >>> Brigham & Women's Hospital, Harvard Medical School >>> Laboratory for Neuroimaging Research >>> One Brookline Place, Suite 602 >>> Brookline, MA 02445, USA >>> Tel: 617-732-6977 >>> Fax: 617-732-6540 >>> Email: delloglio(a)bwh.harvard.edu >>> >> >> > > > -- > Elisa Dell'Oglio, MS > Research Associate to Dr. Bakshi > Brigham & Women's Hospital, Harvard Medical School > Laboratory for Neuroimaging Research > One Brookline Place, Suite 602 > Brookline, MA 02445, USA > Tel: 617-732-6977 > Fax: 617-732-6540 > Email: delloglio(a)bwh.harvard.edu >

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Non-FDR Multiple Corrections for Volume?
by Dave Brohawn 01 Apr '09

01 Apr '09

Hello, I am curious if there are non-FDR multiple comparison correction options available for volume data? I am guessing monte carlos are possible to run for volumetric data, though I am not sure what the input file would be. It wouldn't be the mgh file made from mris_preproc, but what command could create a similar concatenated file using volume data that could produce an input file for the monte carlos? Thanks, Dave Brohawn

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Non-FDR Multiple Corrections for Volume?
by Dave Brohawn 01 Apr '09

01 Apr '09

1 0

tksurfer error
by Elisa Dell'Oglio 01 Apr '09

01 Apr '09

Hi all, I am running freesurfer on CentOS (5.2-x86_64). I get the folowing error when I launch tksurfer: surfer: ### redraw failed: no gl window open. The result is that no surface is shown. Any advice on how to solve the problem? Thanks, Elisa

2 3

Command works in optseq, not optseq2
by Dan Dillon 31 Mar '09

31 Mar '09

Dear FreeSurfers, I'm having a little trouble getting something that works in optseq to work in optseq2. Here's what' is going on . . . when I run this command, things work fine and I get 6 nice sequences: optseq -ntp 170 -TR 3 -npercond 4 4 4 4 4 4 -tpercond 17 17 17 17 17 17 -label NgReal NgLook NgPhoto NuReal NuLook NuPhoto -nsessions 6 -nruns 1 -timewindow 20 -prestim 4 -nsearch 50 -o OptseqTEST However, when I run this command (i.e., my best translation of the previous command into optseq2), I get an error saying that all my schedules are ill-conditioned and I need more scan time or fewer repetitions: optseq2 --ntp 170 --tr 3 --psdwin 0 20 1 --ev NgReal 17 4 --ev NgLook 17 4 --ev NgPhoto 17 4 --ev NuReal 17 4 --ev NuLook 17 4 --ev NuPhoto 17 4 --nsearch 100 --nkeep 6 --o Optseq2TEST Is this a substantive difference between optseq and optseq2 or did I make a mistake with my optseq2 command? Also, I'm assuming there is a reason why I should use optseq2 rather than optseq, but I don't know what it is. Can someone clue me in? Thanks! Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 495-1889 E-mail: <mailto:dillon@wjh.harvard.edu> dillon(a)wjh.harvard.edu

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GM in ROIs
by Kelly Silva 31 Mar '09

31 Mar '09

Hello, Can I calculate GM in ROIs that I have done? How can I do that? Thanks and regards, Kelly Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

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selxavg3-sess error: matrix is singular to working precision
by Jeremy Elman 30 Mar '09

30 Mar '09

Hello all, I am trying to run a first level analysis on a subject with selxavg3-sess but keep running into the same error. The dof file is created, but that is it. Any ideas what might be causing this? Below is the error given. Thank you very much for your help, Jeremy [jelman@psych118 functional]$ selxavg3-sess -s LDR001-1 -analysis LDR-fmcsm4-rec -------------------------------------------------------------- selxavg3-sess logfile is /mtl/LDR/functional/log/selxavg3-sess-bold-LDR-fmcsm4-rec-090326144433.log -------------------------------------------------------------- ------------------------------------------- /mtl/LDR/functional/LDR001-1 Thu Mar 26 14:44:35 PDT 2009 anadir = /mtl/LDR/functional/LDR001-1/bold/LDR-fmcsm4-rec ------------------------------------------ ------- matlab output -------------------- Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. < M A T L A B (R) > Copyright 1984-2008 The MathWorks, Inc. Version 7.6.0.324 (R2008a) February 10, 2008 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> $Id: fast_selxavg3.m,v 1.55.2.6 2008/05/14 20:01:35 greve Exp $ outtop = /mtl/LDR/functional Extension format = nii UseFloat = 0 INFO: acfbins is not set, setting to 10 INFO: mask is not set, setting to brain 1 old-v-new.mat Loaded /mtl/LDR/functional/LDR001-1/bold/007/ldr_paradigm.par as a par4 file. nruns = 2 autostimdur = 1 outanadir = /mtl/LDR/functional/LDR001-1/bold/LDR-fmcsm4-rec Found 155793/475136 (32.8) voxels in mask Creating Design Matrix Loaded /mtl/LDR/functional/LDR001-1/bold/007/ldr_paradigm.par as a par4 file. Warning: Matrix is singular to working precision. > In fast_selxavg3 at 208 Loaded /mtl/LDR/functional/LDR001-1/bold/011/ldr_paradigm.par as a par4 file. Warning: Matrix is singular to working precision. > In fast_selxavg3 at 208 ntptot = 364, nX = 14, DOF = 350 ??? Error using ==> svd Input to SVD must not contain NaN or Inf. Error in ==> cond at 40 s = svd(A); Error in ==> fast_selxavg3 at 239 XCond = cond(XtX); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n

2 1

active volume of surface-based analysis
by Wang, Xin 30 Mar '09

30 Mar '09

Hello, Freesurfer group, In the tutorial of surface-based fMRI analysis, the active volume are calculated from the entire depth of an given active vertex. I do not think it is the best way to measure it since no all activities occupy the entire depth of cortex. A logical way to get accurate active volume is measuring the active verities of multiple planes (e.g., at 0.1 mm distance) and then constructing the active volume from activity on these planes. A option (similar as --projfrac_max) can project the sum of all planes on the surface, and 3D active volume can be viewed in tkmedit. Does Freesurfer currently have commands to achieve something like this procedure? I am looking forward to hearing from you ASAP. Thanks, Xin

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