Hello all,
I’m having difficulties with dwibiascorrect again.
Based on the advice mentioned above, I’m using brain masks to get better results and in fact, it does not work:
dwibiascorrect -force -ants -mask hifi_nodifupdn_brain_mask.nii.gz eddy_corrected_dataup.nii.gz -fslgrad eddy_corrected_dataup.eddy_rotated_bvecs dataup.bval eddy_bias_corrected_dataup.nii.gz
dwibiascorrect:
dwibiascorrect: Note that this script makes use of commands / algorithms that have relevant articles for citation; INCLUDING FROM EXTERNAL SOFTWARE PACKAGES. Please consult the help page (-help option) for more information.
dwibiascorrect:
dwibiascorrect: [WARNING] Output file 'eddy_bias_corrected_dataup.nii.gz' already exists; will be overwritten at script completion
dwibiascorrect: Generated temporary directory: /home/zeydabadi/mz/data//FOD/dwibiascorrect-tmp-Y9T7M5/
Command: mrconvert /home/zeydabadi/mz/data//FOD/eddy_corrected_dataup.nii.gz /home/zeydabadi/mz/data//FOD/dwibiascorrect-tmp-Y9T7M5/in.mif -fslgrad /home/zeydabadi/mz/data//FOD/eddy_corrected_dataup.eddy_rotated_bvecs /home/zeydabadi/mz/data//FOD/dataup.bval
Command: mrconvert /home/zeydabadi/mz/data//FOD/hifi_nodifupdn_brain_mask.nii.gz /home/zeydabadi/mz/data//FOD/dwibiascorrect-tmp-Y9T7M5/mask.mif
dwibiascorrect: Changing to temporary directory (/home/zeydabadi/mz/data//FOD/dwibiascorrect-tmp-Y9T7M5/)
Command: dwiextract in.mif - -bzero | mrmath - mean mean_bzero.mif -axis 3
Command: mrconvert mean_bzero.mif mean_bzero.nii -strides +1,+2,+3
Command: mrconvert mask.mif mask.nii -strides +1,+2,+3
Command: N4BiasFieldCorrection -d 3 -i mean_bzero.nii -w mask.nii -o [corrected.nii,init_bias.nii] -s 4 -b [100,3] -c [1000,0.0]
dwibiascorrect:
dwibiascorrect: [ERROR] Command failed: N4BiasFieldCorrection -d 3 -i mean_bzero.nii -w mask.nii -o [corrected.nii,init_bias.nii] -s 4 -b [100,3] -c [1000,0.0] (dwibiascorrect:130)
dwibiascorrect: Output of failed command:
dwibiascorrect:
dwibiascorrect: Changing back to original directory (/home/zeydabadi/mz/data//FOD)
dwibiascorrect: Script failed while executing the command: N4BiasFieldCorrection -d 3 -i mean_bzero.nii -w mask.nii -o [corrected.nii,init_bias.nii] -s 4 -b [100,3] -c [1000,0.0]
dwibiascorrect: For debugging, inspect contents of temporary directory: /home/zeydabadi/mz/data//FOD/dwibiascorrect-tmp-Y9T7M5/
The input image is a 4D image and mask is a 3D one.
Could someone please elaborate how dwibiascorrection operates?