It comes down to whether you think there will be 0 activation in this area if there are 0 items held in memory. If so, then what you have is fine.
doug Katie Bettencourt wrote: > I'm not sure if that's exactly what I am saying. Basically, there is > an area in the brain (which I am trying to localize) that tracks the > number of items you are holding in memory so that the more items you > hold in memory, the higher the bold activation. We have behavioral > results saying how many items people are holding in each of the > conditions, and we want to use this to get out an area in which the > BOLD activation mirrors this. In Brain Voyager, this is done by > weighting the conditions by the behavior, which is what I am trying to > do here. I'm not sure that that translates exactly into what you are > saying. > > Katie > > On Wed, Dec 8, 2010 at 11:47 AM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > It depends on what you want to test exactly. You can just weight > each presentation and test against fixation as you suggest. This > implies that the response amp is 0 when your weight is 0. If > that's not the case, then you need to make a modification. Let me > know if you need that. > > doug > > Katie Bettencourt wrote: > > 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 <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto: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> > <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 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> > <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>> > <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 > <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: > > 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>>> > <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 > <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> > <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 > <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>>> > <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 > <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> > <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 > <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>>> > <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 > <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> > <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 > <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> > > <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> > > <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>> > <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 > <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> > > <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> > > <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> > <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> > > > > -- 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
