Add data and commands for lesion-analysis tutorial
#21
Conversation
- t2_lesion/t2.nii.gz - T2w image with fake lesion - t2_sc_seg.nii.gz - SC segmentation generated using SCIsegV2 - t2_lesion_seg.nii.gz - lesion segmentation generated using SCIsegV2
There was a problem hiding this comment.
LGTM!
(In the future, I think it would be okay to commit directly to master for sct_tutorial_data PRs, and then update the specific data link for the tutorial in the PR to https://github.com/spinalcordtoolbox/sct_tutorial_data/archive/refs/heads/master.zip. This link will contain all of the data, but it will function the same as the individual link for the purposes of testing the PR, since we plan to cd into the t2_lesion folder anyway.)
The reason I suggest this is that I think we can use the SCT PR as the main "review/approval" site? We can link to the sct_tutorial_data commit for reference. Plus, the sct_tutorial_data changes tend to be pretty simple/straightforward, and if any changes are needed, we can always git rebase the master branch to amend the commit.
I think we can be strict about committing to master for SCT, but be lax on the "side" repos, that way we don't hold up any of the bigger reviews.
|
Thanks, Joshua! Agree. However, it seems I'm not authorized to merge this PR: 
|
joshuacwnewton
deleted the
jv/add_data_for_sct_analyze_lesion_tutorial
branch
* Add new files: - t2_lesion/t2.nii.gz - T2w image with fake lesion - t2_sc_seg.nii.gz - SC segmentation generated using SCIsegV2 - t2_lesion_seg.nii.gz - lesion segmentation generated using SCIsegV2 * batch_single_subject.sh: Update with lesion-analysis * tutorial-datasets.csv: Update with lesion data
* Add new files: - t2_lesion/t2.nii.gz - T2w image with fake lesion - t2_sc_seg.nii.gz - SC segmentation generated using SCIsegV2 - t2_lesion_seg.nii.gz - lesion segmentation generated using SCIsegV2 * batch_single_subject.sh: Update with lesion-analysis * tutorial-datasets.csv: Update with lesion data
## Description This PR adds a new [lesion-analysis tutorial](https://spinalcordtoolbox--4586.org.readthedocs.build/user_section/tutorials/lesion-analysis.html). Figures were pushed in a [parallel PR](spinalcordtoolbox/doc-figures#6) to [spinalcordtoolbox/doc-figures](https://github.com/spinalcordtoolbox/doc-figures). Data were pushed in spinalcordtoolbox/sct_tutorial_data#21 and spinalcordtoolbox/sct_tutorial_data@d1e7c20. ## Linked issues Resolves: #4575 --------- Co-authored-by: Mathieu Guay-Paquet <mathieu.guay-paquet@polymtl.ca> Co-authored-by: Sandrine Bédard <71230552+sandrinebedard@users.noreply.github.com> Co-authored-by: Julien Cohen-Adad <jcohen@polymtl.ca> Co-authored-by: Joshua Newton <joshuacwnewton@gmail.com>
This PR corresponds to the SCT PR spinalcordtoolbox/spinalcordtoolbox#4586.
sct_deepseg -task seg_sc_lesion_t2w_sciandsct_analyze_lesioncommands added to the batch_single_subject.sh scriptThe following files have been added:
t2_lesion/t2.nii.gz- T2w image with fake lesiont2_sc_seg.nii.gz- SC segmentation generated using SCIsegV2t2_lesion_seg.nii.gz- lesion segmentation generated using SCIsegV2