Hi Juan,

The scripts ran to completion and produced output files! However, the coronal mask, and all the EMSPartial_Masking files are empty when I attempt to view them in Slicer. the MID0 files do have viewable output, but the mask is not cut at the ACPC (whole brainmask segmentation). Also, my volume summary value is "29".

The only error in the error log is the following:

 < Failed opening /home/bic/Desktop/1.7.7_output/ABC_Segmentation/T1_stripped_to_template_EMS.affine>


A few questions:

If I provide a brainmask, does it need to binary? the brainmask i provided was from freesurfer, which is not a binary mask.

If I do provide a brainmask, do I need to register/transform the brainmask to ACPC space first?

If I do not provide a brainmask I will need an adult skullstripping atlas. Does your team have any adult skullstripping atlases?

Thanks!
Alex