SCT run batch with Manual segmentation location error

[joshuacwnewton]

Hi Fauziyya,

I tried running this script using sct_run_batch alongside the data you shared, but it gave me an error saying that I was missing the create_right_left_seg_mask.py script.

Other than that, there seem to be no errors. So, just to clarify: Is the main issue you’re asking about just the “identifying compression” issue that you described in your most recent email? (In other words, have your other questions been resolved?)

Kind regards,
Joshua

[Mfauziyya]

Correct, not sure if the identification of the compression command was correct. Can you please share the output file you got from the sct_compute_compression command?

Thank you,
Fauziyya

[Mfauziyya]

Also, could you help with the process of identification of region of compression on the MT files based oj the data I shared?

Thank you

Fauziyya

[joshuacwnewton]

@joshuacwnewton

This is a strange bug, though. I would expect sct_register_to_template to internally reorient all of the input images to the same orientation before any processing. So, I don’t quite understand why reorienting the segmentation to ASR fixes the issue. I will need to do some further investigation in order to improve things on SCT’s end. I’ll follow up once I’ve identified the root cause here.

Just to give a quick update: This bug has been fixed as part of the newest SCT release, v6.2.

Thank you kindly for reporting this initial issue!

Kind regards,
Joshua