Hello SCT team,
To calculate DTI metrics, I did all the analysis steps as you explained in the course on the test data you posted. But the final output is very different from what is expected. I am sure that I have done all the steps correctly and I have checked the output of each step.
I have attached the output.
dti_AD.nii.gz (29.8 KB)
dti_FA.nii (33.2 KB)
dti_MD.nii.gz (29.8 KB)
dti_RD.nii.gz (25.2 KB)
Hi @omidetemadi,
I confirm that the DTI metrics you attached are not those expected from the SCT course. There is likely some differences between what you did and the SCT course script, so in order for us to be able to help you, we first need to be able to reproduce exactly what you did. So, could you please include a SHELL script with all the commands you ran, that we can conveniently execute to generate the DTI metrics.
Best
@omidetemadi could you please also add in your script the syntax to download the data? Just to make sure we will be using the same data you’ve used.
And can you also run the following command so we can try to reproduce your issue using the exact same SCT version you’ve been using:
sct_version
Attached is my Shell script, and the results. My SCT version is 5.8
The results got better. I don’t know how this happened. I used the same data last time. Would you please check my results? I want to make sure that the algorithm I am using to calculate the DTI metrics is correct so that I can use this algorithm on my own data.
dti_AD.nii.gz (177.9 KB)
dti_FA.nii.gz (166.4 KB)
dti_MD.nii.gz (179.0 KB)
dti_RD.nii.gz (158.8 KB)
m_AD_in_wm.csv (978 Bytes)
m_FA_in_wm.csv (954 Bytes)
m_MD_in_wm.csv (978 Bytes)
m_RD_in_wm.csv (980 Bytes)
test_sct.sh (5.4 KB)
Thank You
Hi @omidetemadi,
I noticed in your script that you downloaded the course material from 2021-11-16, which was tested on SCT v5.4:
Given that you are using SCT v5.8, it is possible that you are not obtaining the same results as in this old course.
My suggestion would be that you follow the tutorials, which includes similar material, but it is always up-to-date.
Have you already tried that? Are you more comfortable to use the PDF slides? It would be helpful for us to get some feedback on the course/tutorial, so we know what works best for our users 
Actually, no, I have not used it yet. Firstly I watched your course on Youtube and after that, I used the PDF slides.