I noticed that this came up while running BDP. I assume this is not related to the masks that I trace during the cortical extraction procedure? Is there something I was supposed to do that I didn’t?
DWI mask is not defined in input flags. BDP will try to estimate a (pseudo) mask
from 0-diffusion (b=0) image. Automatic mask estimation may not be accurate in
some sitations and can affect overall quality of co-registration. In case
co-registration is not accurate, you can define a DWI mask by using flag
--dwi-mask <mask_filename>. The mask can be generated and hand edited in
BrainSuite interface. This mask would be used only for registration purposes
(and not for statistics computation).
Saved (pseudo) masks: /home/dniuser/Desktop/Scan2_15b_SbjAtlas/s7923AD_JG/s7923AD_JG.dwi.RAS.mask.nii.gz
No, this is not related to the mask for T1w/MPRAGE image. For registration, BDP needs to use an approximate brain-mask for diffusion data. This mask can be defined via --dwi-mask flag. When it not defined then BDP shows this message.
It is recommended to check the automatically estimated mask after processing, as large inaccuracies in the DWI-mask can affect the registration and distortion correction. In case of inaccurate estimation, the DWI-mask should be manually edited and BDP should be re-run with --dwi-mask flag.