Hi Katie, this is a problem in version 4 in which the scaling is a little weird. It has no effect on the statistics (ie, p-values), but when you extract the percent signal change, they appear to be very low. This has been fixed in 5.X. For 4.X, you will need to compute a scaling factor. This can be done in matlab with the following commands:
cd session/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; You would then multiply your % signal change that you get from the ROI analysis by scalefNew. doug Katie Bettencourt wrote: > Hi all, > > I'm doing ROI analysis on functional data with an anatomical label, > and while the activity looks strong and robust in tksurfer, the % > signal changes I am getting are very low (and much lower than we've > previously found), and I'm not sure what's going on. > > I'm running Freesurfer 4.5 on red hat linux. > > The design is a blocked design with 4 non-null conditions, baseline is > fixation. Attached is a picture of the activity I get for 2 subjects > for on of the conditions vs fixation (baseline) at a p<0.05 threshold > with the ROI outlined in black as well as the output from > roisummary-sess for these two subjects in that roi. I calculate % > signal change based of the output from roisummary-sess, dividing each > condition by the baseline in that file and then multiplying by 100. % > signal changes are listed below, along with all commands run. > > % signal change: > 110222SKJ_connected 110222SP_connected > 0.000988998467052 0.000533852720367 > 0.00105349836708 0.000556814127695 > 0.000408499366826 0.000327200054419 > 0.000440749316839 0.000436266739225 > > commands: > mkanalysis-sess -analysis connect -TR 2 -paradigm connect.dat > -designtype blocked -funcstem fmc -motioncor -runlistfile > connect_runs.txt -inorm -tpexclude tpexclude.dat -nconditions 4 > -timewindow 20 -gammafit 2.25 1.25 -noautostimdur > > mkcontrast-sess -analysis connect -contrast connected_vs_unconnected > -a 1 -c 2 > mkcontrast-sess -analysis connect -contrast connected_vs_noise -a 1 -c 3 > mkcontrast-sess -analysis connect -contrast connected_vs_phase -a 1 -c 4 > mkcontrast-sess -analysis connect -contrast connected_vs_fix -a 1 -c 0 > mkcontrast-sess -analysis connect -contrast unconnected_vs_noise -a 2 -c 3 > mkcontrast-sess -analysis connect -contrast unconnected_vs_phase -a 2 -c 4 > mkcontrast-sess -analysis connect -contrast unconnected_vs_fix -a 2 -c 0 > mkcontrast-sess -analysis connect -contrast noise_vs_phase -a 3 -c 4 > mkcontrast-sess -analysis connect -contrast noise_vs_fix -a 3 -c 0 > mkcontrast-sess -analysis connect -contrast shape_vs_noise -a 1 -a 2 -c 3 > mkcontrast-sess -analysis connect -contrast shape_vs_phase -a 2 -a 1 -c 4 > mkcontrast-sess -analysis connect -contrast shape_vs_noisephase -a 2 > -a 1 -c 3 -c 4 > mkcontrast-sess -analysis connect -contrast act_vs_fix -a 2 -a 1 -a 3 > -a 4 -c 0 > > selxavg3-sess -sf connect-sess -df connect.dir -analysis connect > > #run ROIs > setenv anal connect > foreach roi ( infIPS supIPS loc ) > foreach h (lh rh) > func2roi-sess -roidef ${roi}-${anal}-${h} -analysis $anal -anatlabel > ips_loc/${roi}-${h} -sf connect-sess -df connect.dir > roisummary-sess -sumfile ips-rois/${anal}_${roi}-${h}.dat -roidef > ${roi}-${anal}-${h} -analysis ${anal} -sf connect-sess -df connect.dir > python roi_reader.py -r ${roi} -a ${anal} -z ${h} -f ips-rois -c 4 > end > end > > Thanks, > > Katie > > > ------------------------------------------------------------------------ > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------ > > _______________________________________________ > 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.