Hi Paul,

to make mask from dwi_DMC_structural.nii, I used fsl bet command:

bet dwi_proc/dwi_DMC_structural.nii dwi_proc/dwi_DMC_structural_brain.nii -f 0.2 -m -R

the stripping and mask looks fine, while -mask_from_struc option from dwi_DMC_structural.nii generate a very very small mask in many of our images... absolutely useless, I don't know why. Also, the bet generated mask is geometrically fine:

[qcuser@psy10fdc dwi_proc]$ 3dinfo dwi_DMC_structural_brain_mask.nii.gz
++ 3dinfo: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]

Dataset File: dwi_DMC_structural_brain_mask.nii.gz
Identifier Code: NII_tR3h5zs0pRTO3gXHEMKIbg Creation Date: Thu Feb 7 17:09:00 2019
Template Space: ORIG
Dataset Type: Anat Bucket (-abuc)
Byte Order: LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
Storage Mode: NIFTI
Storage Space: 4,622,080 (4.6 million [mega]) bytes
Geometry String: "MATRIX(1.5,0,0,-94.75,0,1.5,0,-99.75,0,0,1.5,-72.75):128,157,115"
Data Axes Tilt: Plumb
Data Axes Orientation:
first (x) = Right-to-Left
second (y) = Anterior-to-Posterior
third (z) = Inferior-to-Superior [-orient RAI]
R-to-L extent: -94.750 [R] -to- 95.750 [L] -step- 1.500 mm [128 voxels]
A-to-P extent: -99.750 [A] -to- 134.250 [P] -step- 1.500 mm [157 voxels]
I-to-S extent: -72.750 -to- 98.250 [S] -step- 1.500 mm [115 voxels]
Number of values stored at each pixel = 1
-- At sub-brick #0 '?' datum type is short


Thanks for your help,

cheers,

Giuseppe