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Add data and commands for lesion-analysis tutorial #21

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Sep 9, 2024
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Add data and commands for lesion-analysis tutorial #21

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valosekj Sep 7, 2024
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batch_single_subject.sh: Update with lesion-analysis
valosekj Sep 7, 2024
7aecb51
tutorial-datasets.csv: Update with lesion data
valosekj Sep 7, 2024
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13 changes: 13 additions & 0 deletions single_subject/batch_single_subject.sh
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Expand Up @@ -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
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3 changes: 3 additions & 0 deletions tutorial-datasets.csv
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Expand Up @@ -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
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