Update the script to SCT v7.0

[valosekj]

Description

This PR aim is to update the script to the new sct v7.2 version. New metric computation were added: Spinal cord metrics (CSA, AP, RL), Canal metrics (CSA, AP, RL), Lesion metrics and aSCOR. Adapting to the new folder organization having different time points per individual, default is set as baseline (ses-M0).

How to test:

Test on sub-001 with default session.

sct_run_batch -path-data ~/datasets/dcm-zurich/ -path-out ~/process_results/dcm-zurich_kahina -script scripts/process_data_dcm-zurich.sh -jobs 1 -include sub-001

Version of SCT : git-master-1e16eb489497137b0f2ce52c08663e4accdb270f

Version of dcm_zurich dataset : 34a6393d74

TODO:

• Jan: review the PR

[sandrinebedard]

thanks @KahinaBch maybe put the following information in the body of the PR instead of just commenting!

This PR aim is to update the script to the new sct v7.2 version. New metric computation were added: Spinal cord metrics (CSA, AP, RL), Canal metrics (CSA, AP, RL), Lesion metrics and aSCOR. To be tested using dcm_zurich data.

You could also add what command to run to test it out.

Here is an example of a PR body: spinalcordtoolbox/spinalcordtoolbox#4948
(look at description, how to test, linked issue sections)

[sandrinebedard]

I tested the PR running the command on the updated version of dcm-zurich:

sct_run_batch -path-data ~/datasets/dcm-zurich/ -path-out ~/process_results/dcm-zurich_kahina -script scripts/process_data_dcm-zurich.sh -jobs 1 -include sub-001

And got the following error:

1/ses-M0_*T2w.*' .
sending incremental file list
rsync: [sender] link_stat "/home/GRAMES.POLYMTL.CA/sebeda/datasets/dcm-zurich/sub-001/ses-M0/anat/sub-001/ses-M0_*T2w.*" failed: No such file or directory (2)

sent 19 bytes  received 12 bytes  62.00 bytes/sec
total size is 0  speedup is 0.00
rsync error: some files/attrs were not transferred (see previous errors) (code 23) at main.c(1330) [sender=3.2.3]
Error: Processing of subject sub-001 failed

I think is because we did not have session in the previous version of dcm-zurich, on what version is the script for?

[sandrinebedard]

thanks for these updates @KahinaBch ! I left some small comments,

We could also consider computing the compression metrics on the spinal canal too (sct_compute_compression)

[sandrinebedard]

Migth also be worth testing using totalspineseg directly on the axial image and compare results!

[sandrinebedard]

this variable is never used

[KahinaBch]

thanks @KahinaBch maybe put the following information in the body of the PR instead of just commenting!

This PR aim is to update the script to the new sct v7.2 version. New metric computation were added: Spinal cord metrics (CSA, AP, RL), Canal metrics (CSA, AP, RL), Lesion metrics and aSCOR. To be tested using dcm_zurich data.

You could also add what command to run to test it out.

Here is an example of a PR body: spinalcordtoolbox/spinalcordtoolbox#4948 (look at description, how to test, linked issue sections)

I just committed a new version that should take new folder format into consideration. The default option is baseline and it should be able to consider a specified timepoints when passed as argument.

[sandrinebedard]

@KahinaBch I just retested the PR on SCT 7.0, and the argument discfile doesn't exist for sct_process_segmentation, is it 7.1 that your script is up-to-date?

I would suggest to describe exactly how to test the script with following details in the PR body:

• What branch
• Command to run
• Which SCT version
• What version of the dataset to use

It would make it easier and making sure I am testing the right thing 😃