Hi Finnegan, there's nothing there that looks wrong with your commands, but I agree that those values look too high. It is possible that some of the 12 voxels in the ROI is causing the problem. If you go into the subject's analysis dir, you'll see a mask there that corresponds to your ROI. You can load that in matlab, find the voxels in the mask, then load the beta.nii.gz and extract out the values from those voxels to see if something looks funny. Also, check to see whether any of the mask falls into ventricle. doug
Finnegan Calabro wrote: > Hi all, we're using 5.1 to analyze some single subject, event-related > functional data, and are getting some strangely high values for % signal > change when using func2roi-sess and roisummary-sess. > > Here are the commands we're running: > > func2roi-sess -s LMV2012_N01_heading -roidef rhmed_singlevsdouble_1 -analysis > glheadgen_analysis -labelfile > /home/vmrao17/freesurfer/subjects/LMV2012_N01/label/rhmed_singlevsdouble_1.label > -maskcontrast allvsoff -maskthresh 1.50 -masktail pos -maskmap sig > > roisummary-sess -sumfile /home/vmrao17/tmp/summary.txt -roidef > rhmed_singlevsdouble_1 -analysis glheadgen_analysis -s LMV2012_N01_heading > > > And this is the output of summary.txt: > > LMV2012_N01_heading > 51 > 12 > 123.737160 > 1.535988 > 1572.000000 > 0.050000 > -0.000000 > 21 > 1 > 0.734151 > 3.595402 > 4.435675 > 5.482294 > 0.544176 > -0.166144 > 2.951724 > 2.114511 > 3.178010 > 2.814232 > 0.944738 > 0.466052 > 8.508595 > 7.646451 > 6.767788 > 9.197896 > 8.802674 > 11.339759 > 7.822568 > 4.040024 > 8.018742 > > The problem is that the effect size values seem very high and/or the baseline > seems very low (e.g., 100*11.33/123.7=9%!). > > In 4.5 we were computing a scaling factor for these values, but my > understanding was that in 5.1 that was no longer needed, correct? Is there > anything else we should be doing differently when computing % signal change > from this output now? The only other strange thing I notice is that the TER > value is 0.05, but documentation describes TR/20 and our TR=2sec, which would > seem to suggest it should be 0.1 instead of 0.05? > > I'm attaching the full output log for the two commands above as well. > Anything that we're obviously doing wrong? Thanks! > > > > ------------------------------------------------------------------------ > > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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.
