dHCP Surface pipeline
Subject:    subjectNN_DTI_0317_MR1-session1
Directory:  /gpfs/home2/fsavvopo/analysis/dHCP_final/NN_DTI_0317_MR1/workdir/subjectNN_DTI_0317_MR1-session1
Threads:    1

/usr/src/structural-pipeline/scripts/surface/pipeline.sh subjectNN_DTI_0317_MR1-session1 -d /gpfs/home2/fsavvopo/analysis/dHCP_final/NN_DTI_0317_MR1/workdir/subjectNN_DTI_0317_MR1-session1 -t 1
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mirtk recon-neonatal-cortex -v --threads=1 --config=/usr/src/structural-pipeline/parameters/recon-neonatal-cortex.cfg --sessions=subjectNN_DTI_0317_MR1-session1 --prefix=surfaces/subjectNN_DTI_0317_MR1-session1/vtk/subjectNN_DTI_0317_MR1-session1 --temp=surfaces/subjectNN_DTI_0317_MR1-session1/vtk/temp-recon/subjectNN_DTI_0317_MR1-session1 --white --pial

Reconstructing cortical surfaces of subjectNN_DTI_0317_MR1 session session1
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=1 --config=/usr/src/structural-pipeline/parameters/recon-neonatal-cortex.cfg --sessions=subjectNN_DTI_0317_MR1-session1 --prefix=surfaces/subjectNN_DTI_0317_MR1-session1/vtk/subjectNN_DTI_0317_MR1-session1 --temp=surfaces/subjectNN_DTI_0317_MR1-session1/vtk/temp-recon/subjectNN_DTI_0317_MR1-session1 --white --pial : failed