Dear Julien,
I am having some trouble when running sct_extract_metric on to extract DTI parameters: even if I go through all the indicated steps, I cannot extract the DTI metrics values (vox, parameter value and ST = 0). You will find the output file attached.
I am using the template and labels obtained from the T2 images I do not manage to figure out if the problem is related to this or not.
I will really appreciate your help.
Thank you in advance!
sct_extract_metric -i /Users/giorgiaquerin/dti_FA.nii.gz -method wa -f /Users/giorgiaquerin/label/atlas -vert 2,7 -vertfile /Users/giorgiaquerin/label/template/PAM50_cord.nii.gz
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Load metric image...
Estimation for label: WM left fasciculus gracilis
Estimation for label: WM right fasciculus gracilis
Estimation for label: WM left fasciculus cuneatus
Estimation for label: WM right fasciculus cuneatus
Estimation for label: WM left lateral corticospinal tract
Estimation for label: WM right lateral corticospinal tract
Estimation for label: WM left ventral spinocerebellar tract
Estimation for label: WM right ventral spinocerebellar tract
Estimation for label: WM left rubrospinal tract
Estimation for label: WM right rubrospinal tract
Estimation for label: WM left lateral reticulospinal tract
Estimation for label: WM right lateral reticulospinal tract
Estimation for label: WM left spinal lemniscus (spinothalamic and spinoreticular tracts)
Estimation for label: WM right spinal lemniscus (spinothalamic and spinoreticular tracts)
Estimation for label: WM left spino-olivary tract
Estimation for label: WM right spino-olivary tract
Estimation for label: WM left ventrolateral reticulospinal tract
Estimation for label: WM right ventrolateral reticulospinal tract
Estimation for label: WM left lateral vestibulospinal tract
Estimation for label: WM right lateral vestibulospinal tract
Estimation for label: WM left ventral reticulospinal tract
Estimation for label: WM right ventral reticulospinal tract
Estimation for label: WM left ventral corticospinal tract
Estimation for label: WM right ventral corticospinal tract
Estimation for label: WM left tectospinal tract
Estimation for label: WM right tectospinal tract
Estimation for label: WM left medial reticulospinal tract
Estimation for label: WM right medial reticulospinal tract
Estimation for label: WM left medial longitudinal fasciculus
Estimation for label: WM right medial longitudinal fasciculus
Estimation for label: GM left ventral horn
Estimation for label: GM right ventral horn
Estimation for label: GM left intermediate zone
Estimation for label: GM right intermediate zone
Estimation for label: GM left dorsal horn
Estimation for label: GM right dorsal horn
Estimation for label: CSF contour
Estimation for label: spinal cord
Estimation for label: white matter
Estimation for label: gray matter
Estimation for label: dorsal columns
Estimation for label: lateral funiculi
Estimation for label: ventral funiculi
Done! To view results, type:
open extract_metric.csv
extract_metric.csv (4.8 KB)