I’m encountering an issue while running the dwibiascorrect command in MRtrix3. I’ve got this error:
user@DESKTOP: my/working/directory$ dwibiascorrect ants dwi.mif dwi_bc.mif 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: Generated scratch directory: /my/working/directory/dwibiascorrect-tmp-UDAIJL/ Command: mrconvert /my/working/directory/dwi.mif /my/working/directory/dwibiascorrect-tmp-UDAIJL/in.mif dwibiascorrect: Changing to scratch directory (/my/working/directory/dwibiascorrect-tmp-UDAIJL/) Command: dwi2mask in.mif mask.mif 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] Command: mrcalc mean_bzero.mif mask.mif -mult - | mrmath - sum - -axis 0 | mrmath - sum - -axis 1 | mrmath - sum - -axis 2 | mrdump - Command: mrcalc corrected.nii mask.mif -mult - | mrmath - sum - -axis 0 | mrmath - sum - -axis 1 | mrmath - sum - -axis 2 | mrdump - dwibiascorrect: [ERROR] mrcalc corrected.nii mask.mif -mult - | mrmath - sum - -axis 0 | mrmath - sum - -axis 1 | mrmath - sum - -axis 2 | mrdump - (ants.py:80) dwibiascorrect: [ERROR] Information from failed command: dwibiascorrect: mrcalc: computing: (corrected.nii * mask.mif)... [==================================================] mrmath: computing sum along axis 0......  mrmath: [ERROR] error creating temporary file in directory "/my/working/directory/dwibiascorrect-tmp-UDAIJL/": No such file or directory mrmath: [ERROR] error creating image "-" mrmath: [ERROR] no filename supplied to standard input (broken pipe?) mrmath: [ERROR] error opening image "-" mrdump: [ERROR] no filename supplied to standard input (broken pipe?) mrdump: [ERROR] error opening image "-" dwibiascorrect: dwibiascorrect: [ERROR] For debugging, inspect contents of scratch directory: /my/working/directory/dwibiascorrect-tmp-UDAIJL/ dwibiascorrect: Scratch directory retained; location: /my/working/directory/dwibiascorrect-tmp-UDAIJL/
I tried this command on WSL2(Ubuntu 20.04.5 LTS).
MRtrix3 version is 3.0.4. (installed from Anaconda.)
ANTs Version is 2.4.4.post34-g7627c44.
Other commands (nii2mif, degibbs, etc.) have worked well so far.
Could you please provide some insights into what might be causing this error and any potential solutions to resolve it? Any help would be greatly appreciated.
Thank you in advance!