Almost successful…perhaps the following errors are related to my previous problems somehow?
I’m getting an auto-masking failure error, which terminates bdp.sh
“BDP encountered an error while estimating the brain-mask for the input diffusion volume…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”
The strange thing is that I am including the –dwi-mask option, see my code below (note, this post shows two hyphens as one). And I rechecked that the mask is anatomically correct.
/mnt/c/Users/Micaceous/Desktop/Research/Programs/BrainSuite17a/bdp/bdp.sh 86_f000_Acute_anat_brain_RAS.bfc.nii.gz –dir=y –tensors –FRACT –t1-mask 86_f000_Acute_anat_brain_RAS.bfc.mask.nii.gz –dwi-mask 86_f000_Acute_dwi_QCed_fixorient_nodif_brain_mask.nii.gz –nii 86_f000_Acute_dwi_QCed_fixorient.nii.gz -g 86_f000_Acute_bvecs_QCed.txt -b 86_f000_Acute_bvals_QCed.txt