Hi,

There isn't an error message, but the end result is problematic. When I inspect the blocks, problems start from volreg.

I extracted the ventricle mask from this link: [afni.nimh.nih.gov]. I don't know if it's a reasonable way to do this but kinda followed this thread:
Create ventricle mask in MNI space

For resampling, I picked a previously preprocessed subject's dataset. It was aligned to MNI152 via @SSwarper and sampled to 3x3x3 mm^3 with a different, more basic afni_proc script. Then I used this code:

3dresample -master sub-10159.rest.nii -prefix ventricle_mask.nii -inset aparc+aseg_REN_vent.nii.gz

-master is the old previously preprocessed dataset. -inset is from that link above (suma_MNI152_2009). So, this was the method.
Right now, I'm trying recon-all again. Will write the results of that too.

Thanks and best regards,
Yasir