Ah, there was one condition (the throw away one) that was all weighted 0, I will just change the weight on that one back to 1. For looking at what shows up in the weighted analysis, if I want to see areas that increase along my weights, would I just make a contrast of all of them vs fixation, and then any area that shows up in that comparison would be an area that followed my weighting (if that makes sense)?
Katie On Tue, Dec 7, 2010 at 4:16 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > They do not need to be whole numbers. 0s should be ok, unless there are > some conditions that only have 0 weighting. For throw aways conditions, you > usually just create a separate condition and leave the weight at 1. > > Katie Bettencourt wrote: > >> It does run ok when the FIR is all weighted to 1. There are weights of 0 >> for the couple conditions that were essentially throwaway trials for >> counterbalancing reasons. Is that what is causing the trouble? Do the >> numbers need to be whole numbers? >> >> katie >> >> On Tue, Dec 7, 2010 at 3:23 PM, Douglas N Greve < >> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> >> It should work in 4.5 too. The numbers are weights. So if you >> think that the response to presentation A of condition 1 will be >> twice that of presentation B of condition 1, then you would have a >> weight of 2 for pres A and 1 for pres B. The weight of fixation >> (condition 0) is unimportant. I can't tell from the error msg >> below whether the error is caused by the weighting or by the FIR. >> Does the FIR run ok when it is not weighted? Are there any task >> weights that are 0? >> >> doug >> >> Katie Bettencourt wrote: >> >> Ah, what I want is the 2nd one then. I was trying to do this >> in freesurfer v 4.5 but I can't figure out how to use the 4th >> column in a way that doesn't crash during selxavg3-sess and >> there isn't much on the wiki about how to use it, what sorts >> of numbers are acceptable in the 4th column? I have 6 >> conditions plus fixation. one condition I want to be ignored >> (so I set the weight to 0), and then I want an increase as set >> size increases but with a plateau at large set sizes. I tried >> weighting them as whole numbers above 1 (which was what >> fixation was set to), weighing them as all less than 1 (but >> with fixation still as 1), weighing them less than 1 and so >> that combined they add up to 1 (fixation still as 1), but all >> errored our in selxavg3-sess. the same data analyzes fine >> unweighted (all 1s in the 4th column of the paradigm file). >> >> This is the output I get when I try to change the 4th column >> of the paradigm file: >> >> selxavg3-sess -s 101103TM_supIPS -df supIPS.dir -analysis >> supIPS-fir-weighted -overwrite >> -------------------------------------------------------------- >> selxavg3-sess logfile is >> >> >> /home/kcb/mri-space/supIPS_loc/log/selxavg3-sess-bold-supIPS-fir-weighted-101207145505.log >> -------------------------------------------------------------- >> ------------------------------------------- >> /home/kcb/mri-space/101103TM_supIPS >> Tue Dec 7 14:55:05 EST 2010 >> anadir = >> /home/kcb/mri-space/101103TM_supIPS/bold/supIPS-fir-weighted >> analysis supIPS-fir-weighted alread exists for 101103TM_supIPS >> ... reanalyzing (deleting old analysis) >> ------------------------------------------ >> ------- 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 1984-2010 The MathWorks, Inc. >> Version 7.10.0.499 (R2010a) 64-bit (glnxa64) >> February 5, 2010 >> >> To get started, type one of these: helpwin, helpdesk, or demo. >> For product information, visit www.mathworks.com >> <http://www.mathworks.com> <http://www.mathworks.com>. >> >> >> >> >> >> >> >> >> >> >> /usr/local/freesurfer4.5/fsfast/toolbox/fast_selxavg3.m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> $Id: fast_selxavg3.m,v 1.55.2.8 2009/04/17 20:09:46 greve Exp $ >> outtop = /home/kcb/mri-space >> Extension format = nii >> UseFloat = 0 >> INFO: mask is not set, setting to brain >> 1 act_vs_fix-delay.mat >> Ignoring stimulus duration for FIR model >> Ignoring stimulus duration for FIR model >> Ignoring stimulus duration for FIR model >> Ignoring stimulus duration for FIR model >> Ignoring stimulus duration for FIR model >> Ignoring stimulus duration for FIR model >> Excluding 2 points >> nruns = 2 >> autostimdur = 0 >> >> >> outanadir = >> /home/kcb/mri-space/101103TM_supIPS/bold/supIPS-fir-weighted >> Found 48212/124416 (38.8) voxels in mask >> Creating Design Matrix >> Ignoring stimulus duration for FIR model >> Ignoring stimulus duration for FIR model >> Ignoring stimulus duration for FIR model >> Ignoring stimulus duration for FIR model >> Ignoring stimulus duration for FIR model >> Ignoring stimulus duration for FIR model >> Excluding 2 points >> Warning: Matrix is singular to working precision. >> > In fast_selxavg3 at 212 >> Ignoring stimulus duration for FIR model >> Ignoring stimulus duration for FIR model >> Ignoring stimulus duration for FIR model >> Ignoring stimulus duration for FIR model >> Ignoring stimulus duration for FIR model >> Ignoring stimulus duration for FIR model >> Excluding 2 points >> Warning: Matrix is singular to working precision. >> > In fast_selxavg3 at 212 >> ntptot = 616, nX = 80, DOF = 536 >> Saving X matrix to >> >> /home/kcb/mri-space/101103TM_supIPS/bold/supIPS-fir-weighted/Xtmp.mat >> ??? 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 248 >> XCond = cond(XtX); >> >> ------------------------------------------ >> ERROR: fast_selxavg3() failed\n >> >> >> >> >> katie >> >> On Tue, Dec 7, 2010 at 2:50 PM, Douglas N Greve >> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: >> >> what are you trying to do exactly? The external regressor is >> usually used with a continuous measure (eg, skin >> conductance, it >> can also be used to seed-based functional connectivity). If you >> expect the hemodynamic response to be scaled by something (eg, >> reaction time), then that should be incorporated into the >> paradigm >> file in the 4th column. >> >> doug >> >> Katie Bettencourt wrote: >> >> So I just need 1 column with a line for each time point >> that >> has the weight I want to give the condition that is >> occuring >> at that time point? And what do you mean a contrast will >> automatically be created for it? I was trying to use >> this to >> find an area that increases with load but then plateaus >> at a >> point where subject's behavioral performance plateaus (so >> essentially looking for a mirroring of the behavioral >> data in >> the neural data), will there just be a contrast created >> after >> I run selxavg3-sess that I can bring up with tksurfer-sess >> afterwards? >> >> katie >> >> On Tue, Dec 7, 2010 at 11:40 AM, Douglas N Greve >> <gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>>>> wrote: >> >> It is just a text file with a value for each time point. >> You can >> have multiple columns, but if it is a task, then you >> probably want >> to keep one to make the interpretation easier. A >> contrast will >> automatically be created for it. You can look at the >> mcprextreg >> file created by the motion correction to get an idea. >> >> doug >> >> Katie Bettencourt wrote: >> >> I'm trying to set up an analysis using an external >> regressor >> (as part of the mkanalysis-sess stream, -taskreg >> flag) in >> version 5, but I'm not sure what the taskreg.dat >> file >> should >> look like. The only thing I can find is that it >> should >> have a >> line for each time point. Does anyone have any more >> guidance >> than this? >> >> Katie >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> <mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.harvard.edu>>> >> >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>>> >> >> Phone Number: 617-724-2358 Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> >> FileDrop: >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> < >> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> < >> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> >> >> >> The information in this e-mail is intended only for the >> person to >> whom it is >> addressed. If you believe this e-mail was sent to you in >> error and >> the e-mail >> contains patient information, please contact the >> Partners >> Compliance HelpLine at >> http://www.partners.org/complianceline . If the >> e-mail was >> sent to >> you in error >> but does not contain patient information, please >> contact the >> sender and properly >> dispose of the e-mail. >> >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>> >> Phone Number: 617-724-2358 Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> FileDrop: >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >> Phone Number: 617-724-2358 Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > >
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