External Email - Use Caution Here is how I made the label into a surface overlay: mri_label2vol --label $label/lh.7Networks_6.label --temp /data/project/vislab/a/HCP_diff_Sara/fsaverage/mri/orig.mgz --identity --o $vols/lh.7Networks_6.nii mri_vol2surf --src $vols/lh.7Networks_6.nii --out $surfs/lh.7Networks_6.mgh --regheader fsaverage --hemi lh
Here is the mri_mask command: mri_mask betamaskedFPcflh.mgh $surfs/lh.7Networks_6.mgh betasigandlabelmaskedFPcflh.mgh Output from mri_mask: DoAbs = 0 INFO: MRImask() using MRImaskDifferentGeometry() Writing masked volume to betasigandlabelmaskedFPcflh.mgh...done. Sara A. Sims, MA Medical/Clinical Psychology Program UAB | The University of Alabama at Birmingham CIRC Suite 252A | 1719 6th Avenue South | Birmingham, AL 35294 P: 205.975.4060 | sno...@uab.edu On 10/14/19, 2:35 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of fis...@nmr.mgh.harvard.edu> wrote: Hi Sara we will need to know the actual commands and the screen output from them that you ran cheers Bruce On Mon, 14 Oct 2019, Sims, Sara A (Campus) wrote: > > External Email - Use Caution > > Freesurfers, > > I am trying to use mri_mask using surface overlays. I made a label into a > volume and then into a surface with 1s inside the label and 0s outside the > label. I want to make a connectivity map surface overlay with values only > within my label overlay. However when I run it, it creates a surface overlay > with only zeros. There is definitely values within the label surface overlay > (I triple checked). > > Code I used: > > Mri_mask original_surface_overlay label_mask new_masked_output > > > > It doesn’t output any errors. > > Here is what it looks like in freeview: > > Original surface overlay (label is outlined in green) > > [IMAGE] > > The label made into a surface overlay (same as the one shown in green > above): > > [IMAGE] > > But this is the output: all zeros even though there was data within the > mask. > > [IMAGE] > > > > Help! > > Sara A. Sims > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer