Hello everyone,
I recently upgrade to 4.0.2 version. I found an error on calculation MTR.
I use the same commands and the same cases calculating MTR; however, 4.0.2 gave error value different from 4.0.0 beta version.
Command:
sct_deepseg_sc -i mt1.nii -c t2 -qc ~/qc_singleSubj
sct_create_mask -i mt1.nii -p centerline,mt1_seg.nii -size 35mm -f cylinder -o mask_mt1.nii
sct_register_multimodal -i mt0.nii -d mt1.nii -dseg mt1_seg.nii -param step=1,type=im,algo=slicereg,metric=CC -m mask_mt1.nii -x spline -qc ~/qc_singleSubj
sct_compute_mtr -mt0 mt0_reg.nii -mt1 mt1.nii
sct_register_multimodal -i $SCT_DIR/data/PAM50/template/PAM50_t2.nii.gz -iseg $SCT_DIR/data/PAM50/template/PAM50_cord.nii.gz -d mt1.nii -dseg mt1_seg.nii -param step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3 -m mask_mt1.nii -initwarp …/t2/warp_template2anat.nii.gz -qc ~/qc_singleSubj
sct_label_utils -i mt1_seg.nii -create-seg -1,4 -o label_c3c4.nii.gz
sct_register_to_template -i mt1.nii -s mt1_seg.nii -ldisc label_c3c4.nii.gz -ref subject -param step=1,type=seg,algo=centermassrot:step=2,type=seg,algo=bsplinesyn,slicewise=1
mv warp_PAM50_t22mt1.nii.gz warp_template2mt.nii.gz
sct_warp_template -d mt1.nii -w warp_template2mt.nii.gz -qc ~/qc_singleSubj
sct_extract_metric -i mtr.nii -l 50 -vert 3:4 -o mtr_in_sc3_4.csv
Results:
4.0.0beta5
2019-10-18 21:22:48 4.0.0-beta.5 /Users/ohlaboratory/Desktop/ris/mt/mtr.nii 2:12 3:4 spinal cord 1915.1919487633800 33.395869749980800 5.913861825314080
4.0.2
2019-10-22 15:55:02 4.0.2 /Users/ohlaboratory/Desktop/ris0203002/mt/mtr.nii 2:12 3:4 spinal cord 1902.0600379818200 178398311743488.0 0.0
Another issue mtr.nii cannot show proper on FSLviewer even though I have adjust the window width/level.
Could you please let me know how to fix these issues?
Thank you again.