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.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 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
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