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