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 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
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Douglas N. Greve, Ph.D.
MGH-NMR Center
greve at nmr.mgh.harvard.edu
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