Hello Freesurfers,
I have developed a pipeline that uses mri_label2vol to take freesurfer parcellations to native fmri space, and uses dilation (within mri_label2vol) to make the ROIs larger since our resolution is only 3.5x3.5x4 we would end up with only a few voxels for some ROIs due to large voxel size and partial voluming wihout the dilation. However, since the lh and rh are done separately by mri_label2vol, I now have overlap on the midline and have to go through a bunch of masking steps to eliminate it.
My question is; is there a tool that will take both lh/rh parcellations to a new coordinate system, do dilation, and most importantly control for lh/rh overlap? Or any other similar suggestions. Thanks!
Basically I am looking to rework my pipeline, and it seems I should be able to find a more parsimonious solution, than my "Rube Goldberg" approach.
Chris