Hi Lingqiang, I did not have a strong reason not to do the low pass filtering. I think I tried it once and it did not seem to make much difference, so I did not implement it in FSFAST. The differences may be due to filtering, but there are a lot of other places where things can be different too. Can you turn off the filtering in spm? doug
kon...@nmr.mgh.harvard.edu wrote: > Thanks Doug. The labels work perfectly now. > > I also have a methodological question about the fsfast connectivity > analysis: functional connectivity analyses in the literature (Biswal, etc) > only looks at low-frequency fluctuations from BOLD signals. After > preprocessing and regressing out nuisance regressors, the BOLD signal is > low-pass filtered (usually 0.01-0.1Hz) before the activity within the > seeds are averaged and calculating the whole brain correlation map. > > I couldn't find anything like that within the fsfast connectivity > processing streamline. Is that something that can be turned on and off ? > If so, is there a reason to do it or not do it? > > > PS. We have ran the same data in the same subject with same seeds using > fsfast connectivity streamline and the SPM functional connectivity toolbox > (Gabrieli lab). The results are somewhat similar but there are also marked > differences. I wonder if the low-pass step has anything to do with that. > > Thank you. > > Lingqiang > > >> Hi Lingqiang, convert your .label file to a volume using mri_label2vol >> for each subject, something like >> >> cd $SUBJECTS_DIR/$subject/mri >> mri_label2vol --label lh.yourlabel.label --temp orig.mgz --regheader >> orig.mgz --subject $subject --hemi lh --proj frac 0 1 .1 --o yourlabel.mgz >> >> When you run fcseed-config specify -segmentation yourlabel.mgz -segid 1 >> >> doug >> >> >> kon...@nmr.mgh.harvard.edu wrote: >> >>> Hi Freesurfers, >>> >>> We are trying to do a resting-state functional connectivity analysis >>> using >>> freesurfer. Instead of using the aparc+aseg segmentations as seeds, we >>> would like to use a subject-specific surface labels that we have defined >>> apriori. >>> >>> In the fcseed-config step, we then don't have a "segid" as in the >>> anatomical seeds case. What should we specify as the -segid and -seg >>> (segmentation)? >>> >>> We also looked into the ROI-based options using "-roi" but this takes >>> seeds from output of "funcroi-config" and requires that we specify a >>> contrast and an analysis. How should we just specify a surface label >>> without generating a new analysis and contrast? >>> >>> Any help or suggestions are appreciated. >>> >>> >>> Lingqiang >>> _______________________________________________ >>> 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 >> >> >> >> > > > -- 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.
