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Command to run designer is: singularity run --nv --bind .:/mnt designer2_main.sif designer -denoise -shrinkage frob -adaptive_patch -rician -degibbs -pf 1 -eddy -rpe_pair ${pa} -normalize -mask -b1correct -scratch /mnt/processing -nocleanup ${dwi} ${dwi_out}
Error:
... B1 correction...
Command: dwibiascorrect ants -bias biasfield.mif working.mif dwibc.mif
designer: [ERROR] dwibiascorrect ants -bias biasfield.mif working.mif dwibc.mif (designer_func_wrappers.py:981)
designer: [ERROR] Information from failed command:
designer:
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: /mnt/processing/designer-tmp-7FS5E1/dwibiascorrect-tmp-28GBWG/
Command: mrconvert /mnt/processing/designer-tmp-7FS5E1/working.mif /mnt/processing/designer-tmp-7FS5E1/dwibiascorrect-tmp-28GBWG/in.mif
dwibiascorrect: Changing to scratch directory (/mnt/processing/designer-tmp-7FS5E1/dwibiascorrect-tmp-28GBWG/)
Command: dwi2mask legacy in.mif mask.mif
dwibiascorrect: [ERROR] Could not find ANTS program N4BiasFieldCorrection; please check installation
designer:
designer: [ERROR] For debugging, inspect contents of scratch directory: /mnt/processing/designer-tmp-7FS5E1/
designer: Scratch directory retained; location: /mnt/processing/designer-tmp-7FS5E1/
It looks like ANTs is not installed in the singularity (or docker) image. I don't know if this is the correct place to submit this issue, if not, please let me know where best to submit an issue with the docker container.
Thanks in advance!
The text was updated successfully, but these errors were encountered:
Singularity container metadata:
Command to run designer is:
singularity run --nv --bind .:/mnt designer2_main.sif designer -denoise -shrinkage frob -adaptive_patch -rician -degibbs -pf 1 -eddy -rpe_pair ${pa} -normalize -mask -b1correct -scratch /mnt/processing -nocleanup ${dwi} ${dwi_out}
Error:
It looks like ANTs is not installed in the singularity (or docker) image. I don't know if this is the correct place to submit this issue, if not, please let me know where best to submit an issue with the docker container.
Thanks in advance!
The text was updated successfully, but these errors were encountered: