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.h... ). 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 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.
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