Sct_qc usage & feature request

HI Julien & SCT team,

Thanks for creating the really useful sct_qc - this will definitely help with checking output previously generated.

I have a quick question and two(!) feature requests: for the purpose of assessing sct_register_to_template I used the following command from within my output folder:

sct_qc -i /Users/jon/sct_4.0.0-beta.5/data/PAM50/template/PAM50_t1.nii.gz -s /Users/jon/sct_4.0.0-beta.5/data/PAM50/template/PAM50_cord.nii.gz -p sct_register_to_template -d anat2template.nii.gz

Is this the correct syntax? The choice of input and destination is a bit weird in this case.

Feature requests :wink:
(1) Would it be possible to restrict the output in the qc report to only those slices in the overlay (here my anat2template), and possibly only show every nth slice?
(2) For the purpose of assessing vertebral alignment on these reports it would be super useful to have a single midline sagittal slice of the template and the registered anatomical, where you could quickly assess the relative positions of the discs on an animated gif. Again this should only cover the rostrocaudal extent of the anatomical (not the whole spinal column).

Please let me know if you need more information.

Best wishes,


hey Jon,

right. I haven’t thought people would use it that way :wink: it makes sense though.

a quick workaround for 1) would be to switch between PAM50 and your input image, i.e.:

sct_qc -i anat.nii.gz -s anat_seg.nii.gz -d template2anat.nii.gz -p sct_register_to_template

let me know if that would work for you. Otherwise, we could implement the proposed feature (would be a bit of a pain to implement though)

(2): yup! definitely a great idea. I’ve been meaning to implement it at some point (also a bit of a pain, but definitely worth the pain)

thanks for the feedback!