Hi Thomas, you may have found a bug in my scale factor calculation. Can you compute the new scale factor as described below? BTW, these issues are fixed in version 5.
cd bold/analysis x = load('X'); tirf = x.flac0.ev(3).tirf; Xirf = x.flac0.ev(3).Xirf; scalefOld = sum(Xirf .* repmat(tirf,[1 size(Xirf,2)])); TR = x.flac0.TR; dt = tirf(2)-tirf(1); scalefNew = sum(Xirf)*TR/dt; Thomas Janssens wrote: > Hello, > > I am trying to calculate the percent signal changes for my monkey data. > I did this by running the command selxavg3-sess and looking at the cespct > values (or equivalently by using h.nii divided by h-offset.nii). > I found in the mailing list that this value should be corrected by a scaling > factor scalef if freesurfer-4.5.0 is used (see below). > > If I apply this correction factor I got values that at first sight look > reasonable but if i calcultate the psc using JIP (the imaging program from > Joe Mandeville), i find different values. > And looking at the raw data I have to conclude that the value from JIP are > the correct ones... > > For example if i look at the same voxel in MT if find: > with JIP: -14.45% > with FS: -8.15 % > notice that the values are negative and pretty large due to the fact that we > use and iron oxide contrast agent. > > If, instead of applying the scaling factor scalef (defined below), I apply > the factor max(x.X(:,1)) as a scaling factor (which according to me is the > maximum value of the convolved design matrix,or 'the EV' in FSL lingo), > then I end up with a value of -15.09%. Which is pretty close to the value > obtained with JIP. > I got the last idea from mumford.fmripower.org/perchange_guide.pdf > > Do you have any clue where the differences come from? or if I am doing > something wrong? > > Also, one of my colleagues used both the gamma model and FIR model to > calculate the percent signal change (psc) for his event-related designed > experiment, and the values are also quite different. > He applied the scaling factor for the values from the gamma model, and didn't > do it for the fir model. What he got is 0.6% signal change if he takes the > peak of the time course (which looks quite ok) that fitted from the FIR model > and 1.5% signal change from the gamma model. It seems that there is more than > 2 times differences between these two values. Is it normal, or we need > another scale factor for the fir model? > > > Thanks for the answers! > > regards, > Thomas Janssens > > > > ps: > My selxavg3-sess analysis was done using the following parameters in the > analysis.cfg file: > > -gammafit 0 8 > -gammaexp 0.3 > -timewindow 40.00000000000000000000 > -prestim 0 > -acfbins 10 > -fix-acf > -autostimdur > -no-fsv3-st2fir > -no-fsv3-whiten > -polyfit 2 > -TER .10000000000000000000 > -autowhiten 30 > -nskip 0 > -fwhm 0 > -rescale 1000 > > > > ---------------------------------------------------------------------------------------------- > >> [Freesurfer] Calculating % Signal Change from roisummary-sess readout >> >> Douglas N Greve >> Wed, 04 Aug 2010 14:25:52 -0700 >> >> >> That's right, though you may/will run into the problem of very small >> values in which case you can use this fix: >> >> cd bold/analysis >> x = load('X'); >> tirf = x.flac0.ev(3).tirf; >> Xirf = x.flac0.ev(3).Xirf; >> scalef = sum(Xirf .* repmat(tirf,[1 size(Xirf,2)])); >> >> scalef will be something like 184. Multiply the percent signal change >> you get by this number. BTW, this problem is fixed in version 5. >> >> doug >> >> >> Adam Nitenson wrote: >> Hi Freesurfers, >> >> I am trying to analyze functional activity in individual subjects. >> The structural constraint is a dACC label and the functional >> constraint is positive activation at a specific timepoint (6 sec >> after stimulus). I was just wondering what the numbers following the >> "# of estimates per condition" row actually represented, and how I >> could convert these to % signal change. I saw in an archived email >> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg00171.html >> that someone mentioned taking those values, dividing by the baseline >> offset value (row 4) and multiplying by 100 to get % signal change. >> Is this a valid method? >> >> >> Adam Nitenson, B.S. >> Brain Genomics Lab >> Massachusetts General Hospital >> > ---------------------------------------------------------------------------------------------- > > > > > > Thomas Janssens, PhD student > Laboratorium voor Neuro- en Psychofysiologie > K.U.Leuven Medical School > Herestraat 49, B-3000 Leuven (Belgium) > phone +32 16 33 00 35 > cell phone +32 494 115 509 > _______________________________________________ > 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 _______________________________________________ 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.