Problem of label disc

The problem is
1)I want to get the value of the Fa of left gm ,left gm ,left lateral gm and left meditation gm and right value for c6 .c6-c7 disc.c7.c7- T1disc. I could calculate the related value of c6 and c7 , but I don’t know how to label the c6-c7 ,and c7-T1 disc. how to modify my script?
Do you think the script is ok?

!/usr/bin/env bash

file_dwi=“TANG_WING_KUN_WIP_DTI_thk7_breath_1_5_2”

file_bvec=${file_dwi}.bvec

file_bval=${file_dwi}.bval

Separate b=0 and DW images

sct_dmri_separate_b0_and_dwi -i ${file_dwi}.nii.gz -bvec ${file_bvec}

sct_propseg -i ${file_dwi}_dwi_mean.nii.gz -c dwi

sct_create_mask -i ${file_dwi}_dwi_mean.nii.gz -p centerline,${file_dwi}_dwi_mean_seg.nii.gz -size 30mm

sct_crop_image -i ${file_dwi}.nii.gz -m mask_${file_dwi}_dwi_mean.nii.gz -o ${file_dwi}_crop.nii.gz

sct_dmri_moco -i ${file_dwi}_crop.nii.gz -bvec ${file_dwi}.bvec -x spline

file_dwi=${file_dwi}_crop_moco

file_dwi_mean=${file_dwi}_dwi_mean

# Segment spinal cord (only if it does not exist)

sct_deepseg_sc -i ${file_dwi_mean}.nii.gz -c dwi -qc qc

file_dwi_seg=${file_dwi_mean}_seg

# # Create labels, assuming that the mid-FOV is centered at C2 vertebral level

sct_label_utils -i ${file_dwi_seg}.nii.gz -create-seg 2,3 -o label_C2.nii.gz

sct_label_utils -i ${file_dwi_seg}.nii.gz -create-seg -2,3 -o label_C2.nii.gz

sct_register_to_template -i ${file_dwi_mean}.nii.gz -s ${file_dwi_seg}.nii.gz -l label_C3.nii.gz -ref subject -c t1 -param step=1,type=seg,algo=centermassrot:step=2,type=im,algo=syn,metric=CC,slicewise=0,smooth=0,iter=3 -qc qc

mv warp_template2anat.nii.gz warp_template2dwi.nii.gz

mv warp_anat2template.nii.gz warp_dwi2template.nii.gz

sct_warp_template -d ${file_dwi_mean}.nii.gz -w warp_template2dwi.nii.gz -qc qc

sct_dmri_compute_dti -i ${file_dwi}.nii.gz -bvec ${file_bvec} -bval ${file_bval} -method standard

sct_maths -i label/atlas/PAM50_atlas_00.nii.gz -add $(for i in seq -w 2 2 36; do echo “label/atlas/PAM50_atlas_${i}.nii.gz”; done) -o label/atlas/PAM50_atlas_left.nii.gz

sct_maths -i label/atlas/PAM50_atlas_01.nii.gz -add $(for i in seq -w 3 2 35; do echo “label/atlas/PAM50_atlas_${i}.nii.gz”; done) -o label/atlas/PAM50_atlas_right.nii.gz

sct_extract_metric -i dti_FA.nii.gz -f label/atlas -l 30,31,32,33,34,35,58,59 -vert 2:3 -perlevel 1 -o DWI_FA.csv -append 1

sct_extract_metric -i dti_MD.nii.gz -f label/atlas -l 30,31,32,33,34,35,58,59 -vert 2:3 -perlevel 1 -o DWI_MD.csv -append 1

sct_extract_metric -i dti_RD.nii.gz -f label/atlas -l 30,31,32,33,34,35,58,59 -vert 2:3 -perlevel 1 -o DWI_RD.csv -append 1

sct_extract_metric -i dti_FA.nii.gz -f label/atlas -l 30,31,32,33,34,35,58,59 -vert 2:3 -o DWI_FA.csv -append 1

sct_extract_metric -i dti_FA.nii.gz -f label/atlas -l 30,31,32,33,34,35,58,59 -vert 3:4 -o DWI_FA.csv -append 1

sct_extract_metric -i dti_MD.nii.gz -f label/atlas -l 30,31,32,33,34,35,58,59 -vert 2:3 -o DWI_MD.csv -append 1

sct_extract_metric -i dti_MD.nii.gz -f label/atlas -l 30,31,32,33,34,35,58,59 -vert 3:4 -o DWI_MD.csv -append 1

sct_extract_metric -i dti_RD.nii.gz -f label/atlas -l 30,31,32,33,34,35,58,59 -vert 2:3 -o DWI_RD.csv -append 1

sct_extract_metric -i dti_RD.nii.gz -f label/atlas -l 30,31,32,33,34,35,58,59 -vert 3:4 -o DWI_RD.csv -append 1

2)what is more , for your script ,
sct_label_utils -i ${file_dwi_seg}.nii.gz -create-seg -1,6 -o label_C6.nii.gz
I don’t know the meaning of the create-seg -1,6 -o label_C6.nii.gz , why you create-seg-1,6 . could you explain for a while ?
and if I want to label the c4( anther file which contains c4,c5, c4-c5,c5-c6). should I change it to create- seg-1,4 ? this is the file .
ZONG,_XIAOLAN_WIP_DTI_thk7_breath-2_5_2.PAR (34.6 KB)

I’ve already answered these questions in previous posts. As mentioned in this post please feel free to contact me to establish a more formal collaboration.

Continuing the discussion from Problem of label disc:

王老师您好:
我是您的同行,我们能交流一下吗

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