dHCP Surface pipeline
Subject:    sub-NYS1553-ses-001
Directory:  /data/workdir/sub-NYS1553-ses-001
Threads:    8

/usr/src/structural-pipeline/scripts/surface/pipeline.sh sub-NYS1553-ses-001 -d /data/workdir/sub-NYS1553-ses-001 -t 8
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mirtk recon-neonatal-cortex -v --threads=8 --config=/usr/src/structural-pipeline/parameters/recon-neonatal-cortex.cfg --sessions=sub-NYS1553-ses-001 --prefix=surfaces/sub-NYS1553-ses-001/vtk/sub-NYS1553-ses-001 --temp=surfaces/sub-NYS1553-ses-001/vtk/temp-recon/sub-NYS1553-ses-001 --white --pial

Reconstructing cortical surfaces of sub-NYS1553-ses session 001
Dividing brain volume into disjoint regions
Resampling brain mask to standard RAS space
Resampling T2-weighted image to standard RAS space
No input T1-weighted image found, using only T2-weighted image
Creating corpus callosum mask from segmentation image
Reconstructing boundary of right cerebral hemisphere segmentation

mirtk recon-neonatal-cortex -v --threads=8 --config=/usr/src/structural-pipeline/parameters/recon-neonatal-cortex.cfg --sessions=sub-NYS1553-ses-001 --prefix=surfaces/sub-NYS1553-ses-001/vtk/sub-NYS1553-ses-001 --temp=surfaces/sub-NYS1553-ses-001/vtk/temp-recon/sub-NYS1553-ses-001 --white --pial : failed