So, which version did you find that ces/sqrt(cesvar) did not equal t? doug
Ben Deen wrote: > Hi Doug, > > Thanks for your response. The comments below all regard question #2, > is this is the only one that still concerns me. > > I actually was using the nowhiten flag in the last analysis I > described, which was run in version 4.5. From looking at the ces, > cesvar, and t images in the contrast directories, I am finding that > the value of t is not equal to ces/sqrt(cesvar), so I believe that > this analysis is producing erroneous t-stats. > > I've checked results from analyses run by other members of my lab, for > which the entire processing stream was performed in fs-fast (my data > was preprocessed in FSL and then modeled with FS-FAST, in case that > matters). Their results do not have this discrepancy, indicating that > something is wrong with the specific commands I'm using. Also, when I > model the data using version 5.1, I also do not see this discrepancy. > > Anyway, this is no longer an issue for me as I'm fine using version > 5.1 for the analyses, but I thought this should be mentioned, in case > in reflects a bug in the older modeling scripts. > > best, > > Ben > > On Thu, Sep 8, 2011 at 2:29 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu> wrote: > >> Ben Deen wrote: >> >>> Hi, >>> >>> I have an update to this query. I tried using mkanalysis-sess instead >>> of the ".new" version, and now I do seem to be able to get rid of >>> intensity normalization and prewhitening (or at least, adding these >>> flags now has an effect on betas/t-stats, and in the expected >>> directions). The code I'm using is >>> >>> mkanalysis-sess -analysis ToMLoc-1 -TR 2 -p para.para -dt blocked -fsd >>> bold -funcstem f -runlistfile runlist1 -polyfit 0 -nc 2 -spmhrf 0 -tw >>> 40 -no-inorm -nowhiten -noautostimdur >>> >>> # mkcontrast stuff here... >>> >>> selxavg3-sess -sf sessid -df sessdir -analysis ToMLoc-1 >>> >>> However, I have a few remaining questions about the results. >>> >>> 1) When I look at the regressors used in the analysis, they have a >>> surprisingly large magnitude -- the HRF peaks at a value of ~20. Is >>> there any way to alter the analysis such that these peaks are >>> comparable to the values used in FSL/SPM, which is around .8, so that >>> beta values will be directly comparable across analyses? If not, I >>> can just scale the betas by the relevant factor, but it would be nice >>> if this were possible. >>> >>> >> No not really. The 5.1 version controls this better (but you still can't set >> a scaling parameter). You can play with the -TER parameter. By default it is >> set to .01, I think, which causes the amplitude to be very large. If your >> events appear on the TR, then try setting it to the TR. >> >>> 2) When I compare the results of this analysis to results obtained >>> with FSL or SPM, I find that the spatial pattern of beta/t-stats is >>> very similar, but the t-stats have a noticeably reduced magnitude >>> across the brain. Is there anything that may differ about FS-FAST's >>> implementation of the GLM, such that t-stats would differ? >>> >>> >> You might try turning off the whitening (--no-whiten I think). >> >>> 3) I saw in a ppt presentation on FS-FAST that the option -hpf can be >>> used to add a highpass temporal filter to the model. However, when I >>> use this option with mkanalysis-new, the script says that the flag >>> isn't recognized. Is there another way to add such a filter? >>> >>> >> It's in the 5.X version. >> doug >> >>> Thanks in advance for any help. Cheers, >>> >>> Ben >>> >>> On Mon, Sep 5, 2011 at 12:00 PM, >>> <freesurfer-requ...@nmr.mgh.harvard.edu> wrote: >>> >>> >>>> Message: 1 >>>> Date: Sun, 4 Sep 2011 13:15:51 -0400 >>>> From: Benjamin Matthew Deen <bd...@mit.edu> >>>> Subject: [Freesurfer] FS-FAST modeling question >>>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> >>>> Message-ID: >>>> >>>> <d0755b22ea5ed64c941ed568237aec8d1764dcc...@expo11.exchange.mit.edu> >>>> Content-Type: text/plain; charset="us-ascii" >>>> >>>> Hi, >>>> >>>> I'm trying to run a model in fs-fast using no intensity normalization and >>>> no autocorrelation correction, for the purpose of comparing results with >>>> other software packages, and comparing results with/without autocorrelation >>>> correction. However, I haven't been able to get this to work so far. I've >>>> tried using the -noinorm and -nowhiten flags for mkanalysis-sess.new, but >>>> these don't seem to have any effect on the results: noinorm doesn't change >>>> the beta values, and nowhiten doesn't change either betas or t-stats, at >>>> all. The commands I'm using are: >>>> >>>> mkanalysis-sess.new -analysis ToMLoc-1 -TR 2 -p para.para -dt blocked >>>> -fsd bold -funcstem f -runlistfile runlist1 -polyfit 0 -nc 2 -spmhrf 0 -tw >>>> 40 -noinorm -nowhiten >>>> >>>> mkcontrast-sess -sf sessid -df sessdir -analysis ToMLoc-1 -contrast cope1 >>>> -a 1 -c 2 >>>> mkcontrast-sess -sf sessid -df sessdir -analysis ToMLoc-1 -contrast cope2 >>>> -a 2 -c 1 >>>> mkcontrast-sess -sf sessid -df sessdir -analysis ToMLoc-1 -contrast cope3 >>>> -a 1 -a 2 -c 0 >>>> mkcontrast-sess -sf sessid -df sessdir -analysis ToMLoc-1 -contrast cope4 >>>> -a 0 -c 1 -c 2 >>>> >>>> selxavg3-sess -sf sessid -df sessdir -analysis ToMLoc-1 >>>> >>>> Any idea what might be going wrong, or how I can get this to work? >>>> Thanks, >>>> >>>> Ben >>>> >>>> >>>> >>>> >>> _______________________________________________ >>> 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: 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 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
