Hope you are fine. I am trying to find DTI parameters for several images, and I was wondering whether there would be a way to obtain the DTI parameters (FA, MD, etc.) for about 100 images faster, not one by one (which takes so much time)?
I am not sure I understand the question. DTI is a mathematical model which is derived from multiple diffusion-weighted volumes. So, e.g. if you input 100 diffusion-weighted images and fit the tensor model, that will produce a single FA image, which is then fast to extract. Now if your question is about extracting FA from, let’s say, 100 different patients, then yes, you can use multi-threading approaches via
sct_run_batch. Example of use case here.
Also, when it comes to measuring the diameter of the spinal cord or canal, could it be measured using the SCT?
Yes, SC diameter (AP and RL) could be measured with SCT. You will find more details in the latest SCT course. As for the spinal canal, this is a bit more tricky because you need a reliable spinal canal segmentation. You can try using
sct_propseg -CSF, then add the SC and spinal canal segmentations and then run
If so, the only way is through finding the CSA, or there exists another more direct approach?
That’s not exactly how
sct_process_segmentation works. It compute the equivalent ellipse per slice and then compute the AP and RL diameters (in addition to other metrics, including CSA).