diff --git a/single_subject/batch_single_subject.sh b/single_subject/batch_single_subject.sh index 00a51db..2f32e2a 100755 --- a/single_subject/batch_single_subject.sh +++ b/single_subject/batch_single_subject.sh @@ -146,6 +146,37 @@ sct_compute_compression -i t2_compressed_seg.nii.gz -vertfile t2_compressed_seg_ +# Registering lumbar data to the PAM50 template +# ====================================================================================================================== +cd ../t2_lumbar + +# Crop full-body image to isolate the lumbar region (lowest 200 axial slices) +sct_crop_image -i t2.nii.gz -zmax 200 + +# Use lumbar-specific `sct_deepseg` model to segment the spinal cord +sct_deepseg -i t2_crop.nii.gz -task seg_lumbar_sc_t2w + + +# Generate labels for the 2 spinal cord landmarks: cauda equinea ('99') and T9-T10 disc ('17') +# Note: Normally this would be done manually using fsleyes' "Edit mode -> Create mask" functionality. (Uncomment below) +# +# fsleyes t2.nii.gz & +# +# However, since this is an automated script with example data, we will place the labels at known locations for the +# sake of reproducing the results in the tutorial. +sct_label_utils -i t2_crop.nii.gz -create 27,80,80,60 -o t2_crop_label.nii.gz +sct_label_utils -i t2_crop_label.nii.gz -create-add 27,76,187,17 -o t2_crop_label.nii.gz + +# Register the image to the template using segmentation and labels +# TODO: Uncomment when https://github.com/spinalcordtoolbox/PAM50/pull/27 gets merged and a new PAM50 release is made. +#sct_register_to_template -i t2_crop.nii.gz \ +# -s t2_crop_seg.nii.gz \ +# -ldisc t2_crop_label.nii.gz \ +# -c t2 -qc qc \ +# -param step=1,type=seg,algo=centermassrot:step=2,type=seg,algo=bsplinesyn,metric=MeanSquares,iter=3,slicewise=0:step=3,type=im,algo=syn,metric=CC,iter=3,slicewise=0 + + + # Registering additional MT data to the PAM50 template # ====================================================================================================================== diff --git a/single_subject/data/t2_lumbar/t2.nii.gz b/single_subject/data/t2_lumbar/t2.nii.gz new file mode 100644 index 0000000..ba47c6d Binary files /dev/null and b/single_subject/data/t2_lumbar/t2.nii.gz differ diff --git a/tutorial-datasets.csv b/tutorial-datasets.csv index 7bb7793..b5e87d3 100644 --- a/tutorial-datasets.csv +++ b/tutorial-datasets.csv @@ -5,6 +5,7 @@ data_vertebral-labeling,single_subject/data/t2/t2_seg.nii.gz data_template-registration,single_subject/data/t2/t2.nii.gz data_template-registration,single_subject/data/t2/t2_seg.nii.gz data_template-registration,single_subject/data/t2/t2_labels_vert.nii.gz +data_lumbar-registration,single_subject/data/t2_lumbar/t2.nii.gz data_shape-metric-computation,single_subject/data/t2/t2_seg.nii.gz data_shape-metric-computation,single_subject/data/t2/label/template/PAM50_levels.nii.gz data_compression,single_subject/data/t2_compression/t2_compressed.nii.gz