Hi Freesurfer experts,
I'm trying to run a functional connectivity analysis using a label that was
created in the volume (vta.label). I have a few questions about how I would do
this (compared to a label created on surface).
Usually, we create a smoothed mask using the commands
mri_label2label --s fsaverage --regmethod surface --hemi {hemi} --srclabel
$SUBJECTS_DIR/fsaverage1/label/{label}.label --trglabel
$SUBJECTS_DIR/fsaverage1/label/junk.label --outmask
/cluster/roffman/users/Stable5_PerRun/fsaverage1/mri/{label}_sm00_bin.mgh
mris_fwhm --i
/cluster/roffman/users/Stable5_PerRun/fsaverage1/mri/{label}_sm00_bin.mgh
--fwhm 4 --smooth-only --o
/cluster/roffman/users/Stable5_PerRun/fsaverage1/mri/{label}_sm04.mgh --s
fsaverage --hemi rh
end
I tried running mri_label2label using --regmethod volume, but the command
window says "ERROR: cannot specify outmask with vol reg method"
Do you know how I can create a smoothed mask from a volume label?
And then once I create the mask, in order to apply the mask from fsaverage to
each individual subject, would I use mri_vol2vol?
Thanks,
Anais
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