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@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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