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Add dseg argument to sct_register_multimodal
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It's necessary for the qc report, otherwise the command throws an error.
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joshuacwnewton committed Aug 3, 2023
1 parent 5406c0d commit ef13af4
Showing 1 changed file with 5 additions and 2 deletions.
7 changes: 5 additions & 2 deletions multi_subject/process_data.sh
Original file line number Diff line number Diff line change
Expand Up @@ -145,9 +145,12 @@ file_mt1="${file_mt1}_crop"
# Tips: here we only use rigid transformation because both images have very
# similar sequence parameters. We don't want to use SyN/BSplineSyN to avoid
# introducing spurious deformations.
sct_register_multimodal -i "${file_mt0}.nii.gz" -d "${file_mt1}.nii.gz" \
sct_register_multimodal -i "${file_mt0}.nii.gz" \
-d "${file_mt1}.nii.gz" \
-dseg "${file_mt1}_seg.nii.gz" \
-param step=1,type=im,algo=rigid,slicewise=1,metric=CC \
-x spline -qc "${PATH_QC}"
-x spline \
-qc "${PATH_QC}"
# Register template->mt1
# Tips: here we only use the segmentations due to poor SC/CSF contrast at the bottom slice.
# Tips: First step: slicereg based on images, with large smoothing to capture
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