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 > > > _______________________________________________ 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.
