Using SCT functions on mouse data

Hello everyone,
I am working with some mouse DTI data. The acquisition protocol is made up of 5 b=0 and 30 b=700 s/mm2 so it is strictly DTI. Moreover, they concern peripheral nervous system, since the target is the sciatic nerve – you have an example in the image attached.

I was wandering whether some SCT functions, such as sct_compute_snr could be used all the same for my data efficiently. Indeed, I would like to estimate SNR with varying acquisitions and compare these estimates.
Besr regards,

Hi Rosella,
yes, you can use some of the SCT functions on non-spinal images, sct_compute_snr being one of them, given that the function is agnostic to the shape/organ (ie: the function essentially computes SNR based on images and a mask).

Thank you very much! Does this hold also for other functions involved in image preprocessing such as sct_dmri_moco?

No, not all of them. Eg: sct_register_to_template is fairly “spinal cord specific”, although we could imagine some tweaking to apply it to other organs (especially if their shape is similar).

As for sct_dmri_moco, yes, it is organ-agnostic.

I see,
thank you very much ! One last question, sct_compute_snr function computes SNR per each slice. Is there an option in the command to obtain the average SNR across all image slices for each subject? I can’t find it in the relative help.
thank you,

One last question, sct_compute_snr function computes SNR per each slice.

No it does not. Mean and STD are computed within an input mask (which could span multiple slices).

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