Hi Ladan

the column of -1s means that the label hasn't been sampled onto to the surface, and shouldn't matter if you are doing a volumetric analysis.

cheers Bruce On Sun, 1 Jan 2017, Ladan Shahshahani wrote:

Dear experts,

I'm trying to create labels for subcortical regions. I want to use these labels to extract time series from resting state fMRI data (I want all of the subcortical time series and I want them to be in mni305 space). I'm not sure if I'm doing the right thing. Here's an example of what I used: mri_cor2label --c $FREESURFER_HOME/subjects/fsaverage/mri.2mm/aseg.mgz --id 255 --l ~/Desktop/CC_Anterior.label

After running this command, attached is the label file I get. The first column is all "-1"s.

any ideas how I can go about doing such thing?

Best, Ladan