what is the error? On 05/04/2015 01:56 PM, Xiaomin Yue wrote: > > I am having another problem with mkanalysis-sess, here is my command: > mkanalysis-sess -funcstem fmc.so.sm2 -analysis volanalysis -native > -paradigm human_curv.par -event-related -gammafit 2.25 1.25 > -refeventdur 16 -polyfit 2 -TR 2 -nconditions 8 -fsd bold -per-run > -tpexclude xy_tpexclude. > > it got erros as running selxxavg3-sess. It turns out that the > analysis.info under volanalysis directory has the following "nurisreg > mcextreg 3". Since the data was processing as per run, there is no > mcextreg, but mcprextreg file. The analysis file generated for > surface based analysis has correct analysis.info with mcprextreg. I > am using fs5.3. Did I do anything wrong with the mkanalysis-sess command? > > Thanks, > Xiaomin > > ------------------------------------------------------------------------ > > On Sun, May 3, 2015 at 8:55 AM -0700, "Douglas Greve" > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > If you just want to exclude those time points then you can use a time > point exclude file. To do this, create a text file with the time in > seconds of the time points you want to exclude (t=0 is first time > point), put this file in the run folder (where the raw data is) then > when making the analysis, specify -tpexclude filename. If you want to > create a nuisance regressor, then create a text file with a value for > each time point and put it in the run folder then run mkanalysis-sess > with -nuisreg filename 1 > > doug > > On 5/3/15 11:17 AM, Xiaomin Yue wrote: > > Hi Doug, > > Thanks for your response. I want to treat it as a nuisance > variable. If so, should the #3 is best choice? > > Xiaomin > > ------------------------------------------------------------------------ > Date: Sun, 3 May 2015 11:06:01 -0400 > From: gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > To: freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] a mkanalysis-sess question > > > #1 and #3 are basically the same. If used as a task regressor, > then a contrast for it will be created. #2 is a parametric > modulation. Probably not what you want but see > http://freesurfer.net/fswiki/FsFastParametricModulation > > Do you want to treat it as a nuisance variable or task? In any > event, I would probably recode it to make fixation=0 and > non-fixation something else > > > On 5/2/15 5:34 PM, Xiaomin Yue wrote: > > Hi, > > I have a question related to how to make an appropriate design > matrix using fs-fast 5.3. Subjects’ eye movement was > collected during an experiment. Then, the data has been > transformed to a continuous variable with a number for each > TR. The better fixation performance has higher number. For > example, a number would be 0 if subjects look away from a > target within a TR. In ideal situation, subjects should keep > his eyes on target all the time, so the variable should be 1 > for all TR. According to mkanalysis-sess documents, it seems > that there are three different ways to take into account of > eye fixation performance: 1) use it as an external task > regressor; 2) use it as a weight in the paradigm file (the > fourth column); 3) use it as a nuisance regressor. My > question is what’s the difference between the three methods? > In my situation, which one is the best choice in my situation? > > > I hope the question is clear. Thanks so much for your help. > > > Xiaomin > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ Freesurfer mailing > list Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 > <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. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ Freesurfer mailing > list Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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. > _______________________________________________ Freesurfer mailing > list Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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. > > > _______________________________________________ > Freesurfer mailing list > 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 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
