I mean to take all the values (eg, .68849, .31061, etc), compute their mean, then subtract the mean from each value. This will not affect the slope calculation but can affect the offset. Seeing differences in the offsets does not mean that anything is fundamentally wrong.
doug On 10/29/2013 10:44 AM, Suzanne Oosterwijk wrote: > Hi Doug, > > Attached is the Xtmp.mat file for the analysis that gets the error. > > Thanks for your response on the second question. I am not sure what > you mean with demeaning, so I guess that I am not doing that :-) I > just wanted to make sure that not getting the same results does not > indicate a fundamental problem in my paradigm files. > > Thanks! > Suzanne > > > On Tue, Oct 29, 2013 at 3:31 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > Hi Suzanne, can you send me the Xtmp.mat file that gets created? > > On your second question, the answer might be a little tricky. > First, are you demeaning the modulation value? If not, then you > can certainly get different maps. The other part is that you can > get unpredicatable results because the design matrix is not > orthogonalbecause you have several event types. > > doug > > > > On 10/28/2013 12:30 PM, Suzanne Oosterwijk wrote: > > Hi Doug, > > I am running parametric modulation analyses in which I am > modeling 5 different ratings given by participants in response > to images. To model these ratings I made paradigm files > defining both the onset and the slope for each trial (see > email exchange below). Since I have 5 different ratings, I > made 5 different paradigm files per participant, per run. > These paradigm files hold the exact same trial sequence, only > with different numbers for the slope condition. When running > selxavg3-sess I get the following error: > > Input to SVD must not contain NaN or Inf. > > Error in cond (line 36) > s = svd(A); > > Error in fast_selxavg3 (line 279) > XCond = cond(XtX); > > The strange thing is that selxavg3-sess stops running at a > particular participant when I am trying to model one > particular rating, whereas the exact same analysis for the > other three ratings I have run so far (for the same > participant) does not result in an error. I checked the > paradigm files over and over but I cannot find the mistake. > The paradigm files are all the same in terms of timing and > condition codes etc., the only thing that is different between > the files are the specific ratings per trial. So I really > don't understand why I get this error. I attached the paradigm > files for the erroneous analysis and also for the analysis > that runs successfully. I also attached the selxavg3-sess > logfile for the an erroneous analysis and for the successful > one. Maybe I am missing something here, but I just don't see it. > > Also, I have one other question concerning the parametric > modulation. As I understand it modeling the onset is the same > analysis as a normal contrast comparing a particular condition > against baseline. I compared the onset significance maps > (comparing onset to baseline) for each separate rating, and to > my surprise they are not the same. Since only the ratings > differ between the different analyses, and not the onset times > of the stimuli, I expected those maps to be completely > identical. Am I right in this assumption, or is there a reason > they can be different? > > Thanks! > Suzanne > > > > On Thu, Aug 15, 2013 at 4:28 PM, Douglas 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: > > Hi Suzanne, that is fine > doug > > > > On 8/14/13 7:13 AM, Suzanne Oosterwijk wrote: > > Hi Doug, > > Just a follow-up question. The ratings that I > collected for the > parametric modulation analysis have a range from 0 to > 1. This > means that the weights for some stimuli will have the > value 0. Is > this a problem? I am asking just to make sure that a > weight of 0 > does not exclude the corresponding data-point. > > Thanks, > Suzanne > > > On Fri, Jul 26, 2013 at 7:14 PM, Douglas 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: > > Hi Suzanne, yes that looks correct. > doug > > > > On 7/26/13 9:27 AM, Suzanne Oosterwijk wrote: > > Hello all, > > I want to perform a parametric modulation > analysis in > Freesurfer and I have a question about how to > adapt my > paradigm file. I understand how to code the > offset and the > slope (by adding the individual ratings as the > slope > weight), but I just want to check whether I am > correctly > modelling the trials of no interest. > > I have presented people with negative, > positive and neutral > images all preceded by a fixation cross. I > have individual > ratings for the negative images that I want to > use for the > parametric modulation analysis, but I don't > have any ratings > for the positive and neutral images. I do want > to model > these images and the fixation cross, however, > to make sure > that do not become part of the null. Based on > the wiki I > adapted my paradigm file like this: > > (1 = offset for the negative image; 2 = slope > for the > negative image; 3 = neu/pos image of no > interest; 4 = fixation) > > 00121NULL > 12431fix > 15131negoffset > 1523.79negslope > 18431fix > 21331neu/pos > 24431fix > 27131negoffset > 27231.00negslope > 30431fix > 33131negoffset > 3323.49negslope > 36091NULL > etc. > > Is this correct? > > Thanks so much for responding! > Suzanne > > > > -- > Suzanne Oosterwijk, Ph.D. > > Postdoctoral Researcher > > Department of Social Psychology > > University of Amsterdam > > s.oosterwijk@u <mailto:s.oosterw...@neu.edu > <mailto:s.oosterw...@neu.edu>>va.nl <http://va.nl> > <http://va.nl> > > > https://sites.google.com/site/suzanneoosterwijk/ > > __._,_.___ > Reply via web post > > > <http://groups.yahoo.com/group/martinos-tech/post;_ylc=X3oDMTJwM2ltbGk0BF9TAzk3MzU5NzE0BGdycElkAzQ5ODAyNjAEZ3Jwc3BJZAMxNzA1NzI4NjExBG1zZ0lkAzU4MzAEc2VjA2Z0cgRzbGsDcnBseQRzdGltZQMxMzc0ODQ1MjUy?act=reply&messageNum=5830> > Reply to sender > <mailto:suzanne.oosterw...@gmail.com > > <mailto:suzanne.oosterw...@gmail.com>?subject=Re%3A%20parametric%20modulation> > Reply to group > <mailto:martinos-t...@yahoogroups.com > > <mailto:martinos-t...@yahoogroups.com>?subject=Re%3A%20parametric%20modulation> > Start a New Topic > > > <http://groups.yahoo.com/group/martinos-tech/post;_ylc=X3oDMTJlMGwxMWZ1BF9TAzk3MzU5NzE0BGdycElkAzQ5ODAyNjAEZ3Jwc3BJZAMxNzA1NzI4NjExBHNlYwNmdHIEc2xrA250cGMEc3RpbWUDMTM3NDg0NTI1Mg--> > Messages in this topic > > > <http://groups.yahoo.com/group/martinos-tech/message/5830;_ylc=X3oDMTM0bWtjcmt0BF9TAzk3MzU5NzE0BGdycElkAzQ5ODAyNjAEZ3Jwc3BJZAMxNzA1NzI4NjExBG1zZ0lkAzU4MzAEc2VjA2Z0cgRzbGsDdnRwYwRzdGltZQMxMzc0ODQ1MjUyBHRwY0lkAzU4MzA-> > > > (1) > > Recent Activity: > > Visit Your Group > > > <http://groups.yahoo.com/group/martinos-tech;_ylc=X3oDMTJlNWFnMGY0BF9TAzk3MzU5NzE0BGdycElkAzQ5ODAyNjAEZ3Jwc3BJZAMxNzA1NzI4NjExBHNlYwN2dGwEc2xrA3ZnaHAEc3RpbWUDMTM3NDg0NTI1Mg--> > > Yahoo! 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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. > > > > > -- > Suzanne Oosterwijk, Ph.D. > > Postdoctoral Researcher > > Department of Social Psychology > > University of Amsterdam > > s.oosterwijk@u <mailto:s.oosterw...@neu.edu > <mailto:s.oosterw...@neu.edu>>va.nl <http://va.nl> > <http://va.nl> > > https://sites.google.com/site/suzanneoosterwijk/ > > > > > > -- > > Suzanne Oosterwijk, Ph.D. > > Postdoctoral Researcher > > Department of Social Psychology > > University of Amsterdam > > s.oosterwijk@u <mailto:s.oosterw...@neu.edu > <mailto:s.oosterw...@neu.edu>>va.nl <http://va.nl> <http://va.nl> > > https://sites.google.com/site/suzanneoosterwijk/ > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > -- > > Suzanne Oosterwijk, Ph.D. > > Postdoctoral Researcher > > Department of Social Psychology > > University of Amsterdam > > s.oosterwijk@u <mailto:s.oosterw...@neu.edu>va.nl <http://va.nl> > > https://sites.google.com/site/suzanneoosterwijk/ > -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
