DTI images not display

Hello Everyone,

I have computed DTI using this following commands below.

I found that some case did not show MD, RD, and AD on FSL (attached images).

sct_maths -i dmri.nii -mean t -o dmri_mean.nii

sct_propseg -i dmri_mean.nii -c dwi -qc ~/qc_singleSubj

sct_create_mask -i dmri_mean.nii -p centerline,dmri_mean_seg.nii -size 35mm

sct_crop_image -i dmri.nii -m mask_dmri_mean.nii -o dmri_crop.nii

sct_dmri_moco -i dmri_crop.nii -bvec bvecs.txt

sct_propseg -i dmri_crop_moco_dwi_mean.nii -c dwi -qc ~/qc_singleSubj

sct_register_multimodal -i $SCT_DIR/data/PAM50/template/PAM50_t1.nii.gz -iseg $SCT_DIR/data/PAM50/template/PAM50_cord.nii.gz -d dmri_crop_moco_dwi_mean.nii -dseg dmri_crop_moco_dwi_mean_seg.nii -param step=1,type=seg,algo=centermass:step=2,type=seg,algo=bsplinesyn,slicewise=1,iter=3 -initwarp …/t2/warp_template2anat.nii.gz -initwarpinv …/t2/warp_anat2template.nii.gz -qc ~/qc_singleSubj

mv warp_PAM50_t12dmri_crop_moco_dwi_mean.nii.gz warp_template2dmri.nii.gz

mv warp_dmri_crop_moco_dwi_mean2PAM50_t1.nii.gz warp_dmri2template.nii.gz

sct_warp_template -d dmri_crop_moco_dwi_mean.nii -w warp_template2dmri.nii.gz

sct_dmri_compute_dti -i dmri_crop_moco.nii -bval bvals.txt -bvec bvecs.txt

sct_extract_metric -i dti_FA.nii -l 50 -vert 3:4 -o FA_in_sc3_4.csv

Do you know how to fix this?

Thank you again.

Hi @Suradech_Suthiphosuw

this is just a display issue. On FSLeyes, notice the min/max value of your AD for example: the min is 2.24^10-9 and the max is 31.5. Since these values are very small, they all appear in black. Change the max value to something smaller to be able to see any contrast

It works!
Thank you again!

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