Freesurfer November 2007

freesurfer@nmr.mgh.harvard.edu

54 participants
74 discussions

Re: [Freesurfer] Folding Index question
by Rudolph Pienaar 20 Nov '07

20 Nov '07

Hi Graham - First off, your observation that the FI seems correlated with area is completely correct. I'm not sure if you have the FS source code? Anyway, looking at the relevant code in 'mrisurf.c', the MRIScomputeCurvatureIndices(...) function pretty much computes the folding index (fi) as fi += area * Kmax * (Kmax - Kmin) ; and then, once having summed over the surface, simply divides by *pfi = fi / (4.0*M_PI) ; In essence, this is Van Essen's Folding index -- although I personally do have some issues with it. First of all, Van Essen normalizes his measure with 1/4/pi, indicating that the 1/4pi is the "integral for a cylinder the length of which equals its diameter). I seem to think this integral should be (1/2pi)^2, i.e. 1/4/pi^2. Either way, this is merely a fixed constant and doesn't change the behaviour. And irrespective of the 1/4pi or not, the measure is a strict function of "size", or more accurately, the radius of curvature. Since the curvatures run as the inverse of radius, the curvature values in small sulci/gyri can dominate the 'Folding Index', even if they are 'folded' exactly the same as larger sulci/gyri. In fact, there is nothing really related to 'folding' per se in the measure, so it is arguably something of a misnomer - but I fear I am digressing. I know Bruce originally wrote the FI into FS, but based on this quick re-analysis, I'm kind of thinking that we should normalize the fi (and ici for that matter) with the area overwhich each measure measure is computed... *pfi = fi / (4.0*M_PI) / areaCounted; This makes potentially more sense and removes the area dependency. What do you think, Bruce? -=R -- Rudolph Pienaar, M.Eng, D.Eng / email: rudolph(a)nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA

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Re: [Freesurfer] Folding Index question (fwd)
by Rudolph Pienaar 19 Nov '07

19 Nov '07

On Monday 19 November 2007 09:07, Graham wrote: > 1. DVE's description of the FI calc, which it looks like FS implements > (assuming FS's k calcs are faithful -- that code is hard to follow.) Yep - that the code can be hard to follow. Still, you can assume that FS's k calcs are faithful. But on deeper reflection, the FI calculation in FS has a core area-dependency in the code that probably should be normalized out. > > a) Cylindricallity of gyri and sucli do not contribute equally -- one is > emphasized and the other suppressed. (KMax,Kmin = (5,0) --> FI of 25, vs > KMax,Kmin = (0, -5) --> FI of 0; I think these are the gyral and sulcal > versions of the same shape, right?) > Ok - I suspect you need to think of Kmax and Kmin (also known as the principle k1 and k2 curves) in absolute terms when comparing. The sign really only indicates if the surface is curving "inwards" or "outwards", and doesn't convey comparative magnitude. So, in the case where one of the principle curves is -5 and the other is 0, k1=-5 and k2=0 (Kmax=-5 and Kmin=0), resulting in the same values for gyri and sulci. > b) Certain moderate saddle shapes contribute *negatively*, though the > *extreme* saddle shapes contribute *zero*. This I can't immediately comment on, but even if there is contribution from a saddle shape (i.e. k1 should be approximately k2), so the FI should be close to zero. Switching tracks, you might be interested in the re-vamped 'mris_curvature_stats', which has kind of morphed into the main curvature measure tool in FS. This tool now computes several principle curvature functions on a given surface (optionally saving each as a curvature file), and also determines area- and vertex-normalized integrals for the different functions. Furthermore, the functions and integrals are also computed for only positive and negative curves (or Gaussian curvatures) separately, so sulci and gyri are easily distinguishable. One of the measures is a so-called "sharpness function", which is conceptually related to Van Essen's FI: Sharpness = (k1-k2)^2 Van Essen FI = abs(k1)*(abs(k1)-abs(k2)) The sharpness function gives an indication of how sharply folded a gyrus or sulcus is. What version of 'mris_curvature_stats' are you running? It has seen some active development over the past summer, so you might not have the newest version. Give me a shout if you'd like the current dev version. Cheers -=R -- Rudolph Pienaar, M.Eng, D.Eng / email: rudolph(a)nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA

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Error with selxavg-sess
by Leila Reddy 19 Nov '07

19 Nov '07

Hi, I encountered an error with "selxavg-sess -sf sessid -df sessdir -analysis loc-sm3". Looking through the archives I found that others had errors with selxavg-sess but the errors don't seem to be exactly the same as mine. Please let me know if you have any suggestions on how to get this to work. My log file is pasted at the bottom of this email. I use the PowerPC version of freesurferv4.0.1 --------------------------------------------------------------------- FREESURFER_HOME: /Software/freesurfer Build stamp: freesurfer-Darwin-tiger-stable-pub-v4.0.1 Kernel info: Darwin 8.10.0 Power Macintosh --------------------------------------------------------------------- Thanks a lot! Leila selxavg-sess log file $Id: selxavg-sess,v 1.18 2007/01/09 22:41:18 nicks Exp $ uid=1132(lreddy) gid=1132(lreddy) groups=1132(lreddy), 1185(kraskov), 1152(rodri), 1090(psycho) /Users/lreddy/Desktop/Leila-Data/Imagery/imagery_analysis/RSK006 /Software/freesurfer/fsfast/bin/selxavg-sess -sf sessid -df sessdir -analysis loc-test Darwin wagner.klab.caltech.edu 8.11.0 Darwin Kernel Version 8.11.0: Wed Oct 10 18:26:00 PDT 2007; root:xnu-792.24.17~1/RELEASE_PPC Power Macintosh powerpc Sun Nov 18 20:20:37 PST 2007 selxavg: Command not found. ------------------------------------------- /Users/lreddy/Desktop/Leila-Data/Imagery/imagery_data/RSK006 Sun Nov 18 20:20:37 PST 2007 -------------------------------------------------------- /Users/lreddy/Desktop/Leila-Data/Imagery/imagery_data/RSK006/bold selxavg2 -TR 2.0000 -parname loc.para -o loc-test/h -i 011/f -i 021/f -i 025/f -cfg /Users/lreddy/Desktop/Leila-Data/Imagery/imagery_analysis/RSK006/loc-test/analysis.cfg -ipr 3 -pomnibus loc-test/omnibus/fsig -fomnibus loc-test/omnibus/f -------------------------------------------------------- here --- Parsing Config File: /Users/lreddy/Desktop/Leila-Data/Imagery/imagery_analysis/RSK006/loc-test/analysis.cfg ---- -gammafit 2.25 1.25 -timewindow 30 -prestim 6 -polyfit 1 -TER 2 -nskip 0 -fwhm 0 -extreg mcextreg -nextreg 3 -rescale 1000 Logfile is loc-test/h_sxa.log matlab file is /tmp/sxa_6634.m ----------- Matlab file -------------- % Matlab file for selxavg2 Sun Nov 18 20:20:38 PST 2007 % This file may be deleted % /tmp/sxa_6634.m global QuitOnError; QuitOnError = 1; r = fast_selxavg( '-TR', '2.0000', '-parname', 'loc.para', '-o', 'loc-test/h', '-i', '011/f', '-i', '021/f', '-i', '025/f', '-cfg', '/Users/lreddy/Desktop/Leila-Data/Imagery/imagery_analysis/RSK006/loc-test/analysis.cfg', '-ipr', '3', '-pomnibus', 'loc-test/omnibus/fsig', '-fomnibus', 'loc-test/omnibus/f'); if(r==0) fmri_touch('/Users/lreddy/Desktop/Leila-Data/Imagery/imagery_data/RSK006/bold/loc-test/selxavg.ok.6634'); end exit qoe; ----------------------------------- ------------------------------------------ ------- matlab output -------------------- Warning: Unable to open display iconic, MATLAB is starting without a display. You will not be able to display graphics on the screen. Warning: MATLAB is starting without a display, using internal event queue. You will not be able to display graphics on the screen. < M A T L A B > Copyright 1984-2006 The MathWorks, Inc. Version 7.2.0.283 (R2006a) January 27, 2006 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. Warning: Duplicate directory name: /home/lreddy/matlab. > In path at 113 In startup at 380 In matlabrc at 216 >> >> >> >> >> >> $Id: fast_selxavg.m,v 1.40 2007/01/15 02:29:36 greve Exp $ Parsing Arguments RescaleTarget = 1000 UseMRIread = 1, ext = bhdr Checking Parameters nslices = 32 AutoStimDur: 0 StimDur: Number of Runs: 3 Input Volume List 1 011/f 2 021/f 3 025/f Input Pardigm File List 1 011/loc.para 2 021/loc.para 3 025/loc.para Output Volume loc-test/h F Omnibus Volume loc-test/omnibus/f Sig Omnibus Volume loc-test/omnibus/fsig TR 2.000000 TER 2.000000 Total Window 30 PreStim Window 6 Remove Baseline 1 Remove Trend 0 Remove QTrend 0 Rescale Target 1000 nSkip 0 InPlane Res 3 FWHM 0 Hanning Radius 0 Time Offset 0 GammaFit 1 1 2.25 1.25 GammaFit Alpha: 2 SPM HRF: -1 Seg Brain/Air 1 SynthSeed 0 ExtReg File mcextreg NExtReg 3 ExtRegOrthog 0 firstslice 0 nslices 32 nyqreg 0 SynthSeed = 0 Conditions Found (4): 1 2 3 4 Run 1: 32 32 32 32 Run 2: 32 32 32 32 Run 3: 32 32 32 32 Slice 0, 9.29485e-05 -------------- First Pass (Accumulation), 0.000672511 Run 1/3, 0.00150713 Excluding 0 Points: Warning: Divide by zero. > In fast_selxavg at 440 Loading 011/f Run 2/3, 3.50438 Excluding 0 Points: Warning: Divide by zero. > In fast_selxavg at 440 Loading 021/f Run 3/3, 6.90937 Excluding 0 Points: Warning: Divide by zero. > In fast_selxavg at 440 Loading 025/f Second Pass (Residual Error Estimation), 9.85656 ??? Error using ==> svd NaN or Inf prevents convergence. Error in ==> cond at 40 s = svd(A); Error in ==> fast_selxavg at 239 c = cond(SumXtWX); >> ??? Undefined function or variable 'r'. >> ------------------------------------------ ERROR: fast_selxavg() failed\n ----- End forwarded message -----

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Reading mris_smooth output using Matlab
by Kim Mouridsen 19 Nov '07

19 Nov '07

Hi, We have segmented hippocampus using Freesurfer, and want to generate a surface which can be read into matlab. We use mri_tesselate and mris_smooth. However, the resulting file can not be read into matlab using read_surf. The error we get is ??? Undefined function or variable "vertex_coords". Error in ==> read_surf at 77 vertex_coords = reshape(vertex_coords, 3, vnum)' ; It seems the 'magic' number is 16777213, whereas only 16777214 and 16777215 are supported in read_surf.m How can we read the result of mris_smooth into matlab? Thanks! Kim.

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Folding Index question
by Graham Wideman 16 Nov '07

16 Nov '07

Folks: We're wondering about how FS's "folding index" corresponds to Van Essen's calculation (J Neurosci, 1997 Sept 15). In particular, do the FI values for each region factor out the area of the region or not. When we plot them the FI values look extremely correlated to area, but that doesn't make sense for an index. Ultimately we're wanting to know how to aggregate FIs for individual parcellations into larger regions. Thanks, Graham

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selxavg3 issue
by Keller, Corey J. 16 Nov '07

16 Nov '07

Hi all, I'm running into some problems using the selxavg3-sess command. Previously I ran into a memory issue with matlab while running this command. However, when I run the selxavg-sess command, the analysis completes successfully. This wasn't an issue until I started averaging subjects. It appears that selxavg-sess doesn't create the dof and mask and other files needed for the isxconcat-sess command. Any suggestions? Thanks. Below is my code for selxavg3-sess and selxavg-sess. Best, Corey SELXAVG3 dgow:jsegawa[134] selxavg3-sess -sf sessid03 -df sesspar -analysis simple_v_complex -overwrite -------------------------------------------------------------- selxavg3-sess logfile is /autofs/space/multnomah_003/users/gow/PROZ06/StudyDir/log/selxavg3-sess-bold-sim ple_v_complex-071116113229.log -------------------------------------------------------------- ------------------------------------------- /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003 Fri Nov 16 11:32:29 EST 2007 anadir = /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/simple_v_complex analysis simple_v_complex alread exists for PROZ06003 ... reanalyzing (deleting old analysis) ------------------------------------------ ------- matlab output -------------------- Warning: Unable to open display iconic, MATLAB is starting without a display. You will not be able to display graphics on the screen. Warning: MATLAB is starting without a display, using internal event queue. You will not be able to display graphics on the screen. < M A T L A B > Copyright 1984-2005 The MathWorks, Inc. Version 7.1.0.183 (R14) Service Pack 3 August 02, 2005 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. Adding MNE Toolbox... >> >> >> >> >> >> >> /usr/local/freesurfer/stable4/fsfast/toolbox/fast_selxavg3.m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> $Id: fast_selxavg3.m,v 1.55.2.1 2007/09/27 15:25:58 greve Exp $ outtop = /autofs/space/multnomah_003/users/gow/PROZ06/MRI Extension format = nii UseFloat = 0 INFO: acfbins is not set, setting to 10 INFO: mask is not set, setting to brain 1 allvres.mat 2 omnibus.mat 3 zallvres.mat 4 zomnibus.mat Loaded /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/010/parfile1.par as a par2 file.Ignoring duration for FIR model Ignoring duration for FIR model nruns = 3 autostimdur = outanadir = /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/simple_v_complex Found 41527/110592 (37.5) voxels in mask Creating Design Matrix Loaded /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/010/parfile1.par as a par2 file.Ignoring duration for FIR model Ignoring duration for FIR model Loaded /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/011/parfile1.par as a par2 file.Ignoring duration for FIR model Ignoring duration for FIR model Loaded /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/012/parfile1.par as a par2 file.Ignoring duration for FIR model Ignoring duration for FIR model ntptot = 1242, nX = 24, DOF = 1218 XCond = 56.8839 (normalized) Computing compensation for resdual AR1 bias 1 -0.5 -0.493483 (t=16.1468) 2 -0.25 -0.248851 (t=46.0564) 3 0 -0.00487321 (t=48.3458) 4 0.25 0.237796 (t=78.3629) 5 0.5 0.477198 (t=94.7002) AR1 Correction M: 0.00663368 1.02963 Computing contrast matrices Loaded /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/010/parfile1.par as a par2 file.Ignoring duration for FIR model Ignoring duration for FIR model Loaded /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/010/parfile1.par as a par2 file.Ignoring duration for FIR model Ignoring duration for FIR model Loaded /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/010/parfile1.par as a par2 file.Ignoring duration for FIR model Ignoring duration for FIR model 1 allvres J= 9 eff = 7.7 vrf = 69.6671 vrfffx = 69.2443 r = 1.01 Loaded /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/010/parfile1.par as a par2 file.Ignoring duration for FIR model Ignoring duration for FIR model Loaded /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/010/parfile1.par as a par2 file.Ignoring duration for FIR model Ignoring duration for FIR model Loaded /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/010/parfile1.par as a par2 file.Ignoring duration for FIR model Ignoring duration for FIR model 2 omnibus J=18 eff = 11.1 vrf = 200.1014 vrfffx = 198.7246 r = 1.01 Loaded /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/010/parfile1.par as a par2 file.Ignoring duration for FIR model Ignoring duration for FIR model Loaded /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/010/parfile1.par as a par2 file.Ignoring duration for FIR model Ignoring duration for FIR model Loaded /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/010/parfile1.par as a par2 file.Ignoring duration for FIR model Ignoring duration for FIR model 3 zallvres J= 9 eff = 7.7 vrf = 69.6671 vrfffx = 69.2443 r = 1.01 Loaded /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/010/parfile1.par as a par2 file.Ignoring duration for FIR model Ignoring duration for FIR model Loaded /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/010/parfile1.par as a par2 file.Ignoring duration for FIR model Ignoring duration for FIR model Loaded /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/010/parfile1.par as a par2 file.Ignoring duration for FIR model Ignoring duration for FIR model 4 zomnibus J=18 eff = 11.1 vrf = 200.1014 vrfffx = 198.7246 r = 1.01 OLS Beta Pass run 1 t= 0.0 Loaded /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/010/parfile1.par as a par2 file.Ignoring duration for FIR model Ignoring duration for FIR model run 2 t= 5.3 Loaded /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/011/parfile1.par as a par2 file.Ignoring duration for FIR model Ignoring duration for FIR model run 3 t=10.4 Loaded /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/012/parfile1.par as a par2 file.Ignoring duration for FIR model Ignoring duration for FIR model Global In-Mask Mean = 542.984 Rescale Target = 1000 RescaleFactor = 1.84167 OLS Residual Pass run 1 t= 0.0 Loaded /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/010/parfile1.par as a par2 file.Ignoring duration for FIR model Ignoring duration for FIR model ??? Out of memory. Type HELP MEMORY for your options. Error in ==> fast_selxavg3 at 417 rho1run = sum(rrun(1:end-1,:).*rrun(2:end,:))./rsserun; >> ------------------------------------------ ERROR: fast_selxavg3() failed\n SELXAVG dgow:jsegawa[132] selxavg-sess -sf sessid03 -df sesspar -analysis simple_v_complex INFO: WhitenFlag = 0 -------------------------------------------------------------- selxavg-sess logfile is /autofs/space/multnomah_003/users/gow/PROZ06/StudyDir/log/selxavg-sess-bold-simp le_v_complex-071116111716.log -------------------------------------------------------------- ------------------------------------------- /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003 Fri Nov 16 11:17:17 EST 2007 INFO (PROZ06003): RunList = 010 011 012 -------------------------------------------------------- /autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold selxavg2 -TR 2.8000 -parname parfile1.par -o simple_v_complex/h -i 010/fmc -i 011/fmc -i 012/fmc -cfg /autofs/space/multnomah_003/users/gow/PROZ06/StudyDir/simple_v_complex/analysis. cfg -ipr 3.125 -pomnibus simple_v_complex/omnibus/fsig -fomnibus simple_v_complex/omnibus/f -------------------------------------------------------- here --- Parsing Config File: /autofs/space/multnomah_003/users/gow/PROZ06/StudyDir/simple_v_complex/analysis. cfg ---- -timewindow 25.2 -prestim 0 -polyfit 1 -TER 2.8 -nskip 0 -fwhm 0 -rescale 1000 Logfile is simple_v_complex/h_sxa.log matlab file is /tmp/sxa_31431.m ----------- Matlab file -------------- % Matlab file for selxavg2 Fri Nov 16 11:17:21 EST 2007 % This file may be deleted % /tmp/sxa_31431.m global QuitOnError; QuitOnError = 1; r = fast_selxavg( '-TR', '2.8000', '-parname', 'parfile1.par', '-o', 'simple_v_complex/h', '-i', '010/fmc', '-i', '011/fmc', '-i', '012/fmc', '-cfg', '/autofs/space/multnomah_003/users/gow/PROZ06/StudyDir/simple_v_complex/analysis .cfg', '-ipr', '3.125', '-pomnibus', 'simple_v_complex/omnibus/fsig', '-fomnibus', 'simple_v_complex/omnibus/f'); if(r==0) fmri_touch('/autofs/space/multnomah_003/users/gow/PROZ06/MRI/PROZ06003/bold/simp le_v_complex/selxavg.ok.31431'); end qoe; ----------------------------------- ------------------------------------------ ------- matlab output -------------------- Warning: Unable to open display iconic, MATLAB is starting without a display. You will not be able to display graphics on the screen. Warning: MATLAB is starting without a display, using internal event queue. You will not be able to display graphics on the screen. < M A T L A B > Copyright 1984-2005 The MathWorks, Inc. Version 7.1.0.183 (R14) Service Pack 3 August 02, 2005 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. Adding MNE Toolbox... >> >> >> >> >> >> $Id: fast_selxavg.m,v 1.40.2.1 2007/10/05 21:10:30 greve Exp $ Parsing Arguments RescaleTarget = 1000 UseMRIread = 1, ext = nii Checking Parameters nslices = 27 AutoStimDur: 0 StimDur: Number of Runs: 3 Input Volume List 1 010/fmc 2 011/fmc 3 012/fmc Input Pardigm File List 1 010/parfile1.par 2 011/parfile1.par 3 012/parfile1.par Output Volume simple_v_complex/h F Omnibus Volume simple_v_complex/omnibus/f Sig Omnibus Volume simple_v_complex/omnibus/fsig TR 2.800000 TER 2.800000 Total Window 25.2 PreStim Window 0 Remove Baseline 1 Remove Trend 0 Remove QTrend 0 Rescale Target 1000 nSkip 0 InPlane Res 3.125 FWHM 0 Hanning Radius 0 Time Offset 0 GammaFit 0 GammaFit Alpha: 2 SPM HRF: -1 Seg Brain/Air 1 SynthSeed 0 firstslice 0 nslices 27 nyqreg 0 SynthSeed = 0 Conditions Found (2): 1 2 Run 1: 120 120 Run 2: 120 120 Run 3: 120 120 Slice 0, 5.2e-05 -------------- First Pass (Accumulation), 0.000607 Run 1/3, 0.001506 Excluding 0 Points: Loading 010/fmc Run 2/3, 3.67712 Excluding 0 Points: Loading 011/fmc Run 3/3, 6.96143 Excluding 0 Points: Loading 012/fmc Second Pass (Residual Error Estimation), 10.0999 Paradigm Condition: 51.2312 Var Reduction Range: 197.495 200.118 204.056 Computing hhat Run 1/3, 10.1504 Excluding 0 Points: Run 2/3, 10.4904 Excluding 0 Points: Run 3/3, 10.8313 Excluding 0 Points: Saving offset to simple_v_complex/h-offset_000.bfloat INFO: performing FTest on omnibus NOTE: if this hangs, try running selxavg-sess with the -noomnibus flag. Using MRIread(), which can slow things down. Slice 1, 11.5265 -------------- Slice 2, 13.3047 -------------- Slice 3, 15.0746 -------------- Slice 4, 16.8374 -------------- Slice 5, 18.615 -------------- Slice 6, 20.4063 -------------- Slice 7, 22.2817 -------------- Slice 8, 24.2111 -------------- Slice 9, 26.0804 -------------- Slice 10, 27.9649 -------------- Slice 11, 29.8879 -------------- Slice 12, 31.8154 -------------- Slice 13, 33.7548 -------------- Slice 14, 35.6677 -------------- Slice 15, 37.6064 -------------- Slice 16, 39.4877 -------------- Slice 17, 41.5613 -------------- Slice 18, 43.5031 -------------- Slice 19, 45.4728 -------------- Slice 20, 47.4043 -------------- Slice 21, 49.4282 -------------- Slice 22, 51.3414 -------------- Slice 23, 53.2732 -------------- Slice 24, 55.1614 -------------- Slice 25, 57.0814 -------------- Slice 26, 59.1151 -------------- INFO: saving meta to simple_v_complex/X.mat Done 64.2836 >> >> quiting matlab ------------------------------------------ Fri Nov 16 11:18:35 EST 2007 selxavg2: finished $Id: mkcontrast,v 1.8 2007/07/10 17:19:25 greve Exp $ cmtxfile /autofs/space/multnomah_003/users/gow/PROZ06/StudyDir/simple_v_complex/allvres nconds 2, wcond ndelays 9, wdelay ndelays 9, wpsa sumconds 1 sumdelays 0 nircorr 0 TER 2.8 rdelta rtau Warning: Unable to open display iconic, MATLAB is starting without a display. You will not be able to display graphics on the screen. Warning: MATLAB is starting without a display, using internal event queue. You will not be able to display graphics on the screen. < M A T L A B > Copyright 1984-2005 The MathWorks, Inc. Version 7.1.0.183 (R14) Service Pack 3 August 02, 2005 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. Adding MNE Toolbox... >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> Normalizing contrast matrix >> >> >> >> >> >> >> >> $Id: mkcontrast,v 1.8 2007/07/10 17:19:25 greve Exp $ cmtxfile /autofs/space/multnomah_003/users/gow/PROZ06/StudyDir/simple_v_complex/omnibus nconds 2, wcond ndelays 9, wdelay ndelays 9, wpsa sumconds 0 sumdelays 0 nircorr 0 TER 2.8 rdelta rtau Warning: Unable to open display iconic, MATLAB is starting without a display. You will not be able to display graphics on the screen. Warning: MATLAB is starting without a display, using internal event queue. You will not be able to display graphics on the screen. < M A T L A B > Copyright 1984-2005 The MathWorks, Inc. Version 7.1.0.183 (R14) Service Pack 3 August 02, 2005 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. Adding MNE Toolbox... >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> Normalizing contrast matrix >> >> >> >> >> >> >> >> $Id: mkcontrast,v 1.8 2007/07/10 17:19:25 greve Exp $ cmtxfile /autofs/space/multnomah_003/users/gow/PROZ06/StudyDir/simple_v_complex/zallvres nconds 2, wcond ndelays 9, wdelay ndelays 9, wpsa sumconds 1 sumdelays 0 nircorr 0 TER 2.8 rdelta rtau Warning: Unable to open display iconic, MATLAB is starting without a display. You will not be able to display graphics on the screen. Warning: MATLAB is starting without a display, using internal event queue. You will not be able to display graphics on the screen. < M A T L A B > Copyright 1984-2005 The MathWorks, Inc. Version 7.1.0.183 (R14) Service Pack 3 August 02, 2005 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. Adding MNE Toolbox... >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> Normalizing contrast matrix >> >> >> >> >> >> >> >> $Id: mkcontrast,v 1.8 2007/07/10 17:19:25 greve Exp $ cmtxfile /autofs/space/multnomah_003/users/gow/PROZ06/StudyDir/simple_v_complex/zomnibus nconds 2, wcond ndelays 9, wdelay ndelays 9, wpsa sumconds 0 sumdelays 0 nircorr 0 TER 2.8 rdelta rtau Warning: Unable to open display iconic, MATLAB is starting without a display. You will not be able to display graphics on the screen. Warning: MATLAB is starting without a display, using internal event queue. You will not be able to display graphics on the screen. < M A T L A B > Copyright 1984-2005 The MathWorks, Inc. Version 7.1.0.183 (R14) Service Pack 3 August 02, 2005 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. Adding MNE Toolbox... >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> Normalizing contrast matrix >> >> >> >> >> >> >> >> Started at Fri Nov 16 11:17:16 EST 2007 Ended at Fri Nov 16 11:18:47 EST 2007 COMPLETED SUCCESSFULLY -------------------- Corey Keller Epilepsy Unit Clinical Research Coordinator Massachusetts General Hospital VBK 830, 55 Fruit Street Boston, MA 02114 Phone 802.578.6292 Email cjkeller(a)partners.org ckeller(a)nmr.mgh.harvard.edu

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xtra advice: /usr/local/freesurfer/fsl
by Juranek, Jenifer 16 Nov '07

16 Nov '07

I'm considering downloading and installing fsl_v402 (centos4, 64 bit) I currently have a stable freesurfer_v401 and MNE _v252 on the same workstation. Should the destination directory of the fsl package overwrite the existing directory: /usr/local/freesurfer/fsl Or should I maintain separate environments and install fsl in the fmrib's recommended destination directory: /usr/local/fsl Any advice is greatly appreciated... Jenifer ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~

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loading data to matlab?
by Maryam Vaziri 15 Nov '07

15 Nov '07

Hi, I am a newbie in using freesurfer so sorry if this is a very trivial question. I want to load my fMRI data into matlab. I want to make a matrix containing coordinates and values of all the voxels in the brain at all timepoints. I also only want the voxels that are in the gray matter and not the voxels that are in the white matter or outside the brain. Where can I get this data and how can I load it to matlab? I have already managed to import all the voxels using MRI- ldbvolume, but this includes white matter and skull. How can I get rid of the rest of the brain and just get the surface? Bests, Maryam.

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X11/Tkmedit/Tksurfer Issue
by Lauren Manning 15 Nov '07

15 Nov '07

Hi, I'm using X11 on my Mac OS X to remotely access our Linux machine. When I try and open Tkmedit I get the following error: freeglut (/usr/local/freesurfer/stable/bin/tksurfer.bin): OpenGL GLX extension not supported by display 'localhost:10.0' I've tried using Chicken of the VNC and VNCViewer to remedy this but I still have the same problems. Does anyone know what I should do to fix this? Thanks, Lauren ________________ Lauren N. Manning Senior Clinical Research Assistant Neuroimaging Center McLean Hospital 115 Mill Street Belmont, MA 02478 tel 617.855.2239 fax 617.855.2770 lmanning(a)mclean.harvard.edu

2 1

color of faces of freesurfer's surfaces
by nima＠nmr.mgh.harvard.edu 15 Nov '07

15 Nov '07

Hi, I can read (in Matlab) the freesurfer's coordinates of vertices but can not find how the colors are defined (i.e. colors of sulci versus gyri). Where can I find this information? best Nima

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Freesurfer November 2007