When you say that they are "empty" what do you mean? That there is nothing above threshold or that there is nothing regardless of how low the threshold is? See if you get something if you set the thresh close to 0. Does this happen in the volume and the surface? Have you checked the registration to assure that it is accurate?
On 08/06/2014 06:33 PM, Jiahe Zhang wrote: > Hi Doug, > > I was trying to run functional connectivity analysis following > instructions on the FreeSurferWiki > (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough). > > I was able to successfully run the following commands (nothing errored > as far as I can tell) but the resulting partial correlation and > significance maps turned out to be empty. Could you take a look at the > commands and let me know if anything can be improved? > > 1. PREPROC > preproc-sess -s subject_001 -fwhm 6 -surface fsaverage lhrh > -mni305-2mm -fsd bold -per-run -stc up > > 2. SEED CONFIG > fcseed-config -segid 1010 -fcname L_Posteriorcingulate.dat -fsd bold > -mean -cfg mean.L_Posteriorcingulate.config > > 3. SEED TIMECOURSE > fcseed-sess -s subject_001 -cfg mean.L_Posteriorcingulate.config > > (wm.dat and vcsf.dat were similarly created) > > 4. ANALYSIS CONFIG > mkanalysis-sess -analysis fc.lpccseed.surf.lh.lpf -surface fsaverage > lh -fwhm 6 -notask -taskreg L_Posteriorcingulate.dat 1 -nuisreg > vcsf.dat 5 -nuisreg wm.dat 5 -mcextreg -polyfit 5 -nskip 4 -fsd bold > -TR 5 -per-run -lpf .1 > > 5. ANALYSIS > selxavg3-sess -analysis fc.lpccseed.surf.lh.lpf -s subject_001 > > Thanks, > Jiahe > > > -- > Jiahe Zhang > Ph.D. Student > Department of Psychology > Northeastern University > 617-373-4789 > > > _______________________________________________ > 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 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.
