Manual correction not working properly on SCT course about spinalcordtoolbox

[valosekj]

Working after the latest fixes!

[joshuacwnewton]

Oh, oops! My apologies, I definitely skimmed. Thank you for the correction. I'll update the script accordingly, then. :)

[joshuacwnewton]

Script updated! Please try redownloading the course data by running:

sct_download_data -d sct_course_data -o {path_to_working_directory}

[valosekj]

I believe the corrected label was not picked up because the manual_correction.py does not add -manual anymore. Instead, the corrected label is named derivatives/labels/sub-05/anat/sub-05_acq-MTon_MTS_seg.nii.gz (ie without -manual). The label provenance is tracked in the JSON sidecar.

The reason why we do not use the -manual suffix anymore is described in this issue:

• no -manual suffix is used - to be in line with our convention, we do not use the -manual suffix anymore -- the information about the label provenance is stored in the JSON sidecar

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To fix this issue, we can:

1. update the SCT course process_data.sh to not add -manual when looking for the labels under derivatives/labels (lines 52 and 77 in sct_course_data/multi_subject/process_data.sh)
2. modify manual_correction.py to include -manual again

[jcohenadad]

I would go with "1", if not too late @joshuacwnewton

[joshuacwnewton]

It's not too late! (I named the sct_tutorial_data release with the general name "SCT-Course-20231120". This means that as long as we continue to use this name, no updates are needed on SCT's end, which means that any changes to sct_tutorial_data will not block SCT v6.1.)

1. update the SCT course process_data.sh to not add -manual when looking for the labels under derivatives/labels (lines 52 and 77 in sct_course_data/multi_subject/process_data.sh)

Right now, the script relies on the "-manual" suffix to distinguish between normal segs and corrected segs. Based on the above info, it seems that we would need to change the script to instead look for the presence of a .json sidecar file? (Presuming that non-corrected segs will NOT have the sidecar file.)

[jcohenadad]

Based on the above info, it seems that we would need to change the script to instead look for the presence of a .json sidecar file?

No, I think the difference between a manual and an automatic segmentation is the physical location of the file: a manually corrected file would be located under derivatives/.../. @valosekj can confirm

[valosekj]

Based on the above info, it seems that we would need to change the script to instead look for the presence of a .json sidecar file?

No, I think the difference between a manual and an automatic segmentation is the physical location of the file: a manually corrected file would be located under derivatives/.../. @valosekj can confirm

Exactly! The automatically generated files (e.g., by sct_deepseg) are located in the output/data_processed folder, while the manually corrected files are stored under derivatives/labels/.

So, I believe that the only modification of the process_data.sh script is to remove -manual from lines 52 and 77.

[jcohenadad]

Also working on my end-- thank you for the fix! ❤️