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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

2 1

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 ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~

2 1

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.

1 0

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

3 2

mathematica and freesurfer
by nima＠nmr.mgh.harvard.edu 15 Nov '07

15 Nov '07

Hi, Does anybody have (or know of) functions for reading freesurfer's surface or curvature into Mathematica? Nima

2 1

optseq2 question
by John Herrington 13 Nov '07

13 Nov '07

I'm new to optseq and to rapid E-R designs generally. I have a two questions about it. If it helps, here's my (tentative) design - I'm creating a task with 5 conditions (including rest) with a TR of 2320 ms and trial SOA of 4640 ms (my stimuli are on screen for 1 sec of this time). 1) I've been trying to get clear on the logic behind optimizing rapid E-R designs. My read of this literature has led me to the conclusion that there are two overlapping ways to do it: A) vary SOA from one trial to the next, without necessarily paying much attention to trial ordering, and B) vary the trial ordering in a maximally efficient way while keeping the SOA constant from one trial to the next (this is in effect a "jittering", if one considers the variations in time between trial types that results from the pseudorandomization). One can of course combine A and B, but if my logic holds and read of the literature is correct, you could stick with one or the other and still wind up with a sufficiently optimized design. Is this logic and conclusion correct? If so, your program creates a time series via approach B and not A, yes? 2)I'm somewhat familiar with the concept of efficiency in the context of rapid E-R designs, but I haven't found a good resource that tells me what to do with that statistic, as implemented in your program. In other words, what is a passable efficiency threshold for optseq2? I imagine that, like many parameters one selects in MRI, it might depend on any number of factors... but is there any heuristic to apply to the efficiency number generated by your program to figure out what's good and what's bad? Thanks, John

2 1

qdec 'BadMatch' error work-around
by Nick Schmansky 13 Nov '07

13 Nov '07

Freesurfites, If you are encountering the problem where the 'qdec' app exits stating a 'BadMatch' error, then a work-around is, prior to starting qdec, to type, if using tcsh: setenv XLIB_SKIP_ARGB_VISUALS 1 or if using bash: export XLIB_SKIP_ARGB_VISUALS=1 Graphics will run much slower, as hardware acceleration will be disabled, but the app is at least usable. We are still trying to find a real fix for this problem. This problem seems to occur on newer Linux distributions such as Fedora Core 5. Nick

1 0

Mapping group fMRI on surface
by Martin Kavec 13 Nov '07

13 Nov '07

Hi, I can not find my way to map the results of the FSL fMRI group analysis (FLAME1+2) from different subjects on their average surface. Here is in more details what I have done: 1. fMRI analysis of each subject in FSL 2. group analysis (FLAME1+2) in FSL 3. cortical reconstruction of each subject in FS 4. average subject, surface, volume in FS and I would like to a) project results of 2 on results of 4 b) project an ROI from histological atlas on a) Is this doable? Thanks a lot in advance. Martin

3 6

fmc.mcdat file questions
by Brittany Cassidy 13 Nov '07

13 Nov '07

Hi all, I'm analyzing some motion data and I had a two quick questions about the last two columns of the fmc.mcdat file. According to the wiki, the 9th column is RMS error after correction. Could someone shed some light on what RMS stands for and how it's useful? Also, the 10th column is the total vector motion in mm...is this total before or after motion correction? Thanks in advance! -Brittany

2 1

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