Dear experts,

I'm trying to adopt the HCP pipeline to our own data but at it is originally developed for human adults it fails frequently on my data. A big chunk of the pipeline is based on FreeSurfer so I thought it should be most relevant to ask my question here.

the main problem I have here is that mri_watershed fails so the rest of the pipeline cannot proceed. The errors are usually like below:

****************TEMPLATE DEFORMATION****************

second estimation of the COG coord: x=128,y=131, z=124, r=39161 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^

GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 38180 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = -1043712479 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1117744481 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = -1064196139 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1050954328 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 1062732290 mri_watershed Error: GLOBAL region of the brain empty ! ##################################################################

or

*************************WATERSHED************************** Sorting... mri_watershed Error: Problem in the COG calculation: T1.mgz may not contain properly normalized white-matter. Confirm that T1.mgz has enough white-matter voxels of value 110. If white-matter contains few if any voxels of value 110, try adding wm control-points to nu.mgz, and re-run recon-all. #################################################################

I really appreciate any help or direction.

Thank you! Mahmoud