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sct-pipeline / spine-park

Pipeline for multicontrast analysis in PD patients
MIT License
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Add instructions to perform manual vertebral labeling #27

Closed jcohenadad closed 5 months ago

jcohenadad commented 5 months ago

A video and commands will be useful

Kaonashi22 commented 5 months ago

I'm not sure whether the script is calling the manual vertebral labels (names "sub-xx_T2_label-disc.nii.gz") in the derivatives folder (under the input folder). The automatic vertebral labels are still generated (and maybe used)?

Also, there are two derivatives folders, for the manual vertebral labels and for the masks manually corrected. There might be a conflict when I rerun the pipeline (after manual correction of the masks)

jcohenadad commented 5 months ago

I'm not sure whether the script is calling the manual vertebral labels (names "sub-xx_T2_label-disc.nii.gz") in the derivatives folder (under the input folder).

Thank you for catching this @Kaonashi22 ! issue opened https://github.com/sct-pipeline/spine-park/issues/29

jcohenadad commented 5 months ago

Also, there are two derivatives folders, for the manual vertebral labels and for the masks manually corrected. There might be a conflict when I rerun the pipeline (after manual correction of the masks)

The output derivatives folder should be placed where your input BIDS data are. Where are your two derivatives folders?

Kaonashi22 commented 5 months ago

The derivatives folder containing vertebral labels is located in the input BIDS data. The derivatives folder containing the manually corrected masks should also be in the input BIDS data according to the script. For now, I just changed the name of the second folder to avoid a conflict

jcohenadad commented 5 months ago

The derivatives folder containing vertebral labels is located in the input BIDS data. The derivatives folder containing the manually corrected masks should also be in the input BIDS data according to the script. For now, I just changed the name of the second folder to avoid a conflict

both manual segmentation and labels should be under derivatives/labels/. I'm not sure i understand the conflict given that the file names are different. Here is an example of two labels:

image

Kaonashi22 commented 5 months ago

I actually did the manual vertebral labeling and the mask correction at different moments, that's why I have two derivatives folders. I 'll move the files to one folder