I don't know that there will be a big difference. The surface-based fMRI time course originally comes from the volume of course, so you're not freeing yourself from the voxels. If you want to extract the time course from the surface, you can do it with something like
cd session/bold/002 mri_segstats --slabel subject lh /path/to/label --id 1 --i fmcpr.fsaverage.lh.sm05.nii.gz --avgwf label.timecourse.dat then specify -taskreg label.timecourse.dat 1 when running mkanalysis-sess On 10/04/2016 04:29 PM, ERIK JAHNER wrote: > Dear Free Surfer Experts, > > I have a follow-up question to a previous message sent by Lingqiang > which you responded to on Dec 21st 2011. (I have included a copy of > this message below, but here is a link > https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2011-December/021728.html > > ). In a functional connectivity analysis using a subject specific > SURFACE label defined priori, you suggest using mir_label2vol to > convert the surface label to a volume. However, I would assume that > there is some benefit to using the smoothed values found in a surface > vertices after preprocessing as opposed to voxels. If we use a .mgz > segmentation file this seems to sacrifice the benefits of the free > surfer pipeline. Or.... is this only used for reference and using the > time course stored in the vertices on the surface and not actually > just the 3d volume. > > To clarify my question... Is the functional connectivity processing > stream using the time courses associated with the surface vertices > after smoothing or is it just getting the time course of the voxels > nearest the targeted label vertices? > > Thanks > Erik > > --------------------------------------------------- > 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 > > > konglq at nmr.mgh.harvard.edu > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> 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 at nmr.mgh.harvard.edu > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > />/https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer />//>//>// > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve at nmr.mgh.harvard.edu > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > 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 -- 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.
