Summary of what happened:
After running the dhcp-pipeline to segment a T2w MRI (my data, not from dhcp database), I obtained warnings and errors.
Command used (and if a helper script was used, a link to the helper script or the command generated):
The commands used in terminal was:
docker run --rm -t \
-u $(id -u):$(id -g) \
-v $PWD/data:/data \
biomedia/dhcp-structural-pipeline:latest subject1 session1 40 \
-T2 data/T2w.nii -t 8
Version:
Docker version 20.10.23
Environment (Docker, Singularity, custom installation):
I’m running the pipeline from dockerhub.
Data formatted according to a validatable standard? Please provide the output of the validator:
I used dcm2nii DICOM to NIfTI converter in MATLAB.
Relevant log outputs (up to 20 lines):
< /usr/src/structural-pipeline/dhcp-pipeline.sh subject1 session1 40 -T2 data/T2w.nii -t 8
running segmentation pipeline
/usr/src/structural-pipeline/scripts/segmentation/pipeline.sh /data/workdir/subject1-session1/T2/subject1-session1.nii.gz subject1-session1 40 -d /data/workdir/subject1-session1 -t 8
running additional pipeline
/usr/src/structural-pipeline/scripts/misc/pipeline.sh subject1-session1 40 -d /data/workdir/subject1-session1 -t 8
running surface pipeline
/usr/src/structural-pipeline/scripts/surface/pipeline.sh subject1-session1 -d /data/workdir/subject1-session1 -t 8
Pipeline failed: see log files /data/logs/subject1-session1.surface.log /data/logs/subject1-session1.surface.err for details >
Screenshots / relevant information:
The final log output from “subject1-session1.surface.log”:
< mirtk recon-neonatal-cortex -v --threads=8 --config=/usr/src/structural-pipeline/parameters/recon-neonatal-cortex.cfg --sessions=subject1-session1 --prefix=surfaces/subject1-session1/vtk/subject1-session1 --temp=surfaces/subject1-session1/vtk/temp-recon/subject1-session1 --white --pial : failed >
From the file “subject1-session1.surface.err”:
<Error: Surface outside bounds of input image: surfaces/subject1-session1/vtk/temp-recon/subject1-session1/corpus-callosum-mask.nii.gz>
From the files “subject1-session1.additional.err” and “subject1-session1.segmentation.err”, I obtained warnings:
<Warning: FFD spacing smaller than image resolution!
This may lead to artifacts in the transformation because not all control points are within the vicinity of a voxel center.>
Can you give me some suggestion of what could be going wrong?
Thank you so much in advance!
Tânia