Dear experts,
When I warp the template to the native space, the PAM50 atlas seems different from the DWI images and segmentation mask. I think that this mismatch between PAM50 and the DWI images is affecting the statistics (sct_extract_metrics).
I used sct-4.3.
I used the commands:
sct_register_multimodal -i ../${base}-T2_SAG_resize_seg_labeled.nii -d ${base}_eddy_md_crop.nii -x nn -identity 1
sct_label_utils -i ${base}-T2_SAG_resize_seg_labeled_reg.nii -vert-body 1,10 -o ${base}_dmri_labels.nii.gz
sct_register_to_template -i ${base}_eddy_md_crop.nii -l ${base}_dmri_labels.nii.gz -s /home/jnavas/SPINALCORD/spine_masks/masks_reg_crop_fa/${base}_WholeSpine_Mask2_reg.nii.gz -c t1 -param step=1,type=seg,algo=slicereg,metric=MeanSquares: step=2,type=seg,algo=affine,metric=MeanSquares,gradStep=0.2: step=3,type=im,algo=syn,metric=MI,iter=5,shrink=2
sct_warp_template -d ${base}_eddy_md_crop.nii -w warp_template2anat.nii.gz -a 1 -s 1 -ofolder label
I really appreciate any help you can provide.