Update dataset to support contrast agnostic registration tutorial (#11)

Co-authored-by: Julien Cohen-Adad <jcohen@polymtl.ca>

Author: joshuacwnewton

single_subject/batch_single_subject.sh

@@ -155,7 +155,7 @@ fsleyes mt1.nii.gz -cm greyscale -a 100.0 label/template/PAM50_t2.nii.gz -cm gre
 
 
 
-# Computing MTR
+# Computing MTR using MT0/MT1 coregistration
 # ======================================================================================================================
 
 # Register mt0->mt1 using z-regularized slicewise translations (algo=slicereg)
@@ -169,6 +169,27 @@ sct_compute_mtr -mt0 mt0_reg.nii.gz -mt1 mt1.nii.gz
 
 
 
+# Contrast-agnostic registration
+# ======================================================================================================================
+
+# 1. T2w preprocessing (cropping around spinal cord)
+cd ../t2
+sct_deepseg_sc -i t2.nii.gz -c t2 -qc ~/qc_singleSubj
+sct_create_mask -i t2.nii.gz -p centerline,t2_seg.nii.gz -size 35mm -f cylinder -o mask_t2.nii.gz
+sct_crop_image -i t2.nii.gz -m mask_t2.nii.gz
+
+# 2. T1w preprocessing (cropping around spinal cord)
+cd ../t1
+sct_deepseg_sc -i t1.nii.gz -c t1 -qc ~/qc_singleSubj
+sct_create_mask -i t1.nii.gz -p centerline,t1_seg.nii.gz -size 35mm -f cylinder -o mask_t1.nii.gz
+sct_crop_image -i t1.nii.gz -m mask_t1.nii.gz
+
+# 3. Perform registration
+# NB: `-dseg` is not necessary for registration, but is provided for the `-qc` reporting to help with spinal cord visualization
+sct_register_multimodal -i t1_crop.nii.gz -d ../t2/t2_crop.nii.gz -param step=1,type=im,algo=dl -qc ~/qc_singleSubj -dseg ../t2/t2_seg.nii.gz
+
+
+
 # Gray/white matter: Segmentation
 # ======================================================================================================================
 

tutorial-datasets.csv

@@ -11,6 +11,8 @@ data_coregistration,single_subject/data/t2/warp_template2anat.nii.gz
 data_coregistration,single_subject/data/mt/mt1.nii.gz
 data_mtr-computation,single_subject/data/mt/mt0.nii.gz
 data_mtr-computation,single_subject/data/mt/mt1.nii.gz
+data_contrast-agnostic-registration,single_subject/data/t1/t1.nii.gz
+data_contrast-agnostic-registration,single_subject/data/t2/t2.nii.gz
 data_gm-wm-segmentation,single_subject/data/t2s/t2s.nii.gz
 data_gm-wm-metric-computation,single_subject/data/t2s/t2s_gmseg.nii.gz
 data_gm-wm-metric-computation,single_subject/data/t2s/t2s_wmseg.nii.gz