Hi, thank you. I’m not sure yet how to put my image as http link, I will figure that out. But wouldn’t you also need my dwi and t1 files to see if you can recreate the errors on your end?
So to answer your questions…
– I used the same mask as before
– I tried without the dwi-mask option, still throws an error (see below):
Below is the log output from trying to run BDP without the –dwi-mask option:
BDP Version: 17a (build #0072), released 2017-06-22
================================================================================
Setting up dataset and inputs
================================================================================
Reading input flags…
Checking input files…
Processing data with fileprefix:
/mnt/y/jdelly_dti/DTIpipeline_Version2/86_f000_Acute/86_f000_Acute_anat_brain_RAS
================================================================================
Co-registration and Distortion Correction
================================================================================
Reading the input parameters for co-registration…
Total memory (physical+swap) found: 181.09GB
Checking orientation information…Done
Extracting 0-diffusion (b=0) image from input DWIs…
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).
***************************************
* *
* Error running BDP *
* *
* AUTO-MASKING FAILED *
* *
***************************************
Error message:
BDP encountered an error while estimating the brain-mask for the input diffusion
volume.
Error help/resolution:
Please define a mask for diffusion volume by using flag –dwi-mask
<mask_filename>. The mask can be generated and hand edited in BrainSuite
interface.
***************************************