Have you verified that the Anat-Func registration in FreeSurfer is correct? You can view it with tkregister-sess.
On 06/16/2016 10:26 AM, Martin Juneja wrote: > Hi Dr. Greve, > > I used following command for this: > > mkanalysis-sess -analysis LH_XY.surf.lh > -surface fsaverage lh -fwhm 5 -notask -taskreg LH_XYZ.dat 1 -nuisreg vcsf.dat > 5 -nuisreg wm.dat 5 > > -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 3. > > Thanks. > > On Wed, Jun 15, 2016 at 3:07 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > what was your mkanalysis-sess command? > > On 06/08/2016 02:10 PM, Martin Juneja wrote: > > Dear FreeSurfer and SPM experts, > > > > I am trying to calculate functional connectivity maps using > FreeSurfer > > pipeline: > > > > http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough. > > > > After defining a seed region on raw anatomical image, I > co-registered > > functional data with anatomical data (as reference) and made > sure that > > the seed is at correct place on both anatomical (top left in > attached > > image) and functional (top right) data. Using SPM, I confirmed > > co-registration was fine. > > > > But after running all the steps of FC, looks like the FC maps > are not > > correct: sig.nii.gz at -fthresh 2 3 (shown at bottom left) because I > > am not getting significant FC at seed location. Here, bottom right > > shows the seed location on surface after I convert the seed to > > fsaverage space (for visualization purpose). > > > > Any thoughts, ideas or tips on what went wrong here, would be really > > appreciated. > > > > Thanks. > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://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 <mailto: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. > > > > > _______________________________________________ > 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
