diff --git a/single_subject/batch_single_subject.sh b/single_subject/batch_single_subject.sh index b5c24f7..aee1d2e 100755 --- a/single_subject/batch_single_subject.sh +++ b/single_subject/batch_single_subject.sh @@ -114,6 +114,19 @@ 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 +# Note: Two files are output: +# - t2_sc_seg.nii.gz: the spinal cord segmentation +# - t2_lesion_seg.nii.gz: the lesion segmentation + +# 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 new file mode 100644 index 0000000..ce2d60c Binary files /dev/null and b/single_subject/data/t2_lesion/t2.nii.gz differ diff --git a/single_subject/data/t2_lesion/t2_lesion_seg.nii.gz b/single_subject/data/t2_lesion/t2_lesion_seg.nii.gz new file mode 100644 index 0000000..0981f45 Binary files /dev/null and b/single_subject/data/t2_lesion/t2_lesion_seg.nii.gz differ diff --git a/single_subject/data/t2_lesion/t2_sc_seg.nii.gz b/single_subject/data/t2_lesion/t2_sc_seg.nii.gz new file mode 100644 index 0000000..6d969a7 Binary files /dev/null and b/single_subject/data/t2_lesion/t2_sc_seg.nii.gz differ diff --git a/tutorial-datasets.csv b/tutorial-datasets.csv index 9aa76ca..1599b27 100644 --- a/tutorial-datasets.csv +++ b/tutorial-datasets.csv @@ -7,6 +7,9 @@ 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_lesion-analysis,single_subject/data/t2_lesion/t2_sc_seg.nii.gz +data_lesion-analysis,single_subject/data/t2_lesion/t2_lesion_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