Add data and commands for lesion-analysis tutorial (#21)

* Add new files: - t2_lesion/t2.nii.gz - T2w image with fake lesion - t2_sc_seg.nii.gz - SC segmentation generated using SCIsegV2 - t2_lesion_seg.nii.gz - lesion segmentation generated using SCIsegV2 * batch_single_subject.sh: Update with lesion-analysis * tutorial-datasets.csv: Update with lesion data
spinalcordtoolbox · Sep 19, 2024 · 03c21c3 · 03c21c3
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commit 03c21c3
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diff --git a/single_subject/batch_single_subject.sh b/single_subject/batch_single_subject.sh
@@ -114,6 +114,22 @@ sct_compute_compression -i t2_compressed_seg.nii.gz -vertfile t2_compressed_seg_
 
 
 
+# Lesion analysis
+# ======================================================================================================================
+cd ../t2_lesion
+# Segment the spinal cord and intramedullary lesion using the SCIsegV2 model
+# Note: t2.nii.gz contains a fake lesion for the purpose of this tutorial
+sct_deepseg -i t2.nii.gz -task seg_sc_lesion_t2w_sci -qc ~/qc_singleSubj
+# Note: Two files are output:
+# - t2_sc_seg.nii.gz: the spinal cord segmentation
+# - t2_lesion_seg.nii.gz: the lesion segmentation
+
+# Check results using Fsleyes
+fsleyes t2.nii.gz -cm greyscale t2_sc_seg.nii.gz -cm red -a 70.0 t2_lesion_seg.nii.gz -cm blue-lightblue -a 70.0 &
+
+# Compute various morphometric measures, such as number of lesions, lesion length, lesion volume, etc.
+sct_analyze_lesion -m t2_lesion_seg.nii.gz -s t2_sc_seg.nii.gz -qc ~/qc_singleSubj
+
 # Registering T2 data to the PAM50 template
 # ======================================================================================================================
 cd ../t2

diff --git a/single_subject/data/t2_lesion/t2.nii.gz b/single_subject/data/t2_lesion/t2.nii.gz
diff --git a/tutorial-datasets.csv b/tutorial-datasets.csv
@@ -7,6 +7,7 @@ data_compression,single_subject/data/t2_compression/t2_compressed.nii.gz
 data_normalizing-morphometrics-compression,single_subject/data/t2_compression/t2_compressed_seg.nii.gz
 data_normalizing-morphometrics-compression,single_subject/data/t2_compression/t2_compressed_seg_labeled.nii.gz
 data_normalizing-morphometrics-compression,single_subject/data/t2_compression/t2_compressed_labels-compression.nii.gz
+data_lesion-analysis,single_subject/data/t2_lesion/t2.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