Katie Bettencourt wrote: > Ok, so if I use the 4 col I don't need to use -autostimdur, I can use > -noautostimdur or can I leave it out all together? I think it forces you to choose one. If you have 4 col, then use -noautostimdur > > I noticed that FIR ignored the stimulus duration entirely, so I only > need the -autostimdur/noautostimdur for gamma event related or AB designs? FIR will ignore the duration. For gammafit, the duration is important, but if you have 4col, then use -no-autostimdur. For AB, there is no paradigm file -- you tell it the on and off durations. > > However, I did get a difference (and a fairly large one) for a FIR > event related analysis with 4 col paradigm files when I did > mkanalysis-sess -noautostimdur and mkanalysis-sess -autostimdur. > Should i just ignore the -autostimdur one? Yes, ignore the -autostimdur.
doug > > Katie > > On Fri, Apr 15, 2011 at 2:51 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > Oh, sorry, I had forgotten when I introduced the 4col format. Yes, > 4.5 does take the 4 col. I actually dont remember exactly what 4.5 > does when you give it autostimdur with a 4col. It might ignore the > duration in the parfile and compute it from the stimulus timing. > If you represent all time in your paradigm file, this should do > the same thing. For the FIR, the stimulus duration is ignored > entirely. > > doug > > Katie Bettencourt wrote: > > Wait, I'm confused, in v 4.5 (which I'm using) the paradigm > files have 4 values per line (starting time, condition, > length, and weight), so don't they have the lengths in there? > I know you could use an older paradigm file with only 2 > columns (starting time, condition), and in this case I would > list each TR and the condition there, but the wiki says that > v. 4.5 can use the 4 column paradigm files. Is that not true? > I mean it obviously uses the weights.... > > I ran an event related analysis with -noautostimdur in the > analysis, with a 4 column paradigm file. I did not list every > TR, but used the 3rd column to list the length of time. I got > what appears to be valid data out. When I redid it with > -autostimdur, I got very little activation. But if the > -noautostimdur assumes that each event is equal to the TR > (which is shorter than the actual durations I have), then > wouldn't the analysis have had problems because I didn't cover > all the TRs in the paradigm file? But it worked fine. > > I'm very confused here. > > Also, is there a difference between the way this is used in > FIR and Gamma analyses? > > Katie > > > On Fri, Apr 15, 2011 at 2:33 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: > > FYI: autostimdur is not valid in version 5.X because the > stimulus > duration is supplied in the paradigm file. For earlier > versions, > there was no info in the par file about the duration. The > -autostimdur will compute the duration of the stimulus from the > paradigm file based upon the time to the next stimulus > entry this > works as long as all time is accounted for in the parfile > and no > stimuli overlap. If you use -no-autostimdur, then it will > assume > that the duration of the event is equal to the TR. > > doug > > > Katie Bettencourt wrote: > > I'm a bit confused about what the -autostimdur and > -noautostimdur flags in mkanalysis-sess do. I've > checked the > help files, but the wording is a bit confusing, and > when I run > them on my event related design, I get different results > depending on which flag I use, with the -noautostimdur > being > more of what I expect as far as results go. > > Also, they are only used in event related and AB > designs, not > blocked, correct? > > Katie > > > -- 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> > > > > > 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> > 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
