Surface pipeline failed

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


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/ subject1 session1 40 -T2 data/T2w.nii -t 8

running segmentation pipeline
/usr/src/structural-pipeline/scripts/segmentation/ /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/ subject1-session1 40 -d /data/workdir/subject1-session1 -t 8
running surface pipeline
/usr/src/structural-pipeline/scripts/surface/ 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!