Hi, I'm trying to create a ROI of V1 from the labels (for each hemisphere) I defined. I was able to create an volume with the command below
mri_label2vol --label $SUBJ/label/lh.v1.ali.label --label $SUBJ/label/rh.v1.ali.label --temp $SUBJ/mri/T1.mgz --reg $SUBJ/stats/register.dat --fillthresh 0.5 --o $SUBJ/ROI/test_v1_T_000.bshort
What I want are these 1) This command gives me an ROI which includes the gray matter but I want a smoother ROI which also has some nearby white matter voxels so that I make sure ROI doesn't leave any V1 voxel out for my functional analysis later on. I looked at the --proj flag for this but couldn't find any explanation about it. Would it help me about this? Where can I find more information about it? Would changing --labvoxvol make sense?
2) The resulting ROI is not binary and I would like to make it so (actually left and right hemispheres are in different densities, e.g. one seems lighter and the other one is darker in my viewer). Can I output the volume as binary from mri_label2vol or should I convert it later on (and how)?
Best, Ali