Joshua Newton

Consider re-adding symmetry to the list of metrics computed by `sct_process_segmentation`

1

We used to have "symmetry" as a metric in one of the figures included in the SCT Course/Web Tutorials. The symmetry diagram was recently removed when this figure was re-made...

While investigating https://forum.spinalcordmri.org/t/interpolation-in-the-process-of-registration/1147, I wanted to determine the interpolation used during straightening. At first glance, I thought the answer lay with the [`interpolation_warp`](https://github.com/spinalcordtoolbox/spinalcordtoolbox/blob/75c0672617ec99cfcde60ce0cd39e7e674d0c2ea/spinalcordtoolbox/straightening.py#L31) parameter. However, when I Ctrl+F the project...

Update GitHub Actions workflow files to support Merge Queues

2

GitHub has released their new Merge Queue feature: https://github.blog/changelog/2023-02-08-pull-request-merge-queue-public-beta/ Earlier today, I tried enabling this feature, and we tried enqueuing some open PRs. However, the required checks never fired. Digging...

`sct_extract_metric` contains a number of "Advanced" command line options: https://github.com/spinalcordtoolbox/spinalcordtoolbox/blob/61ed4a71ceca1ad43b1ccffd76ca8c24ec90a1ad/spinalcordtoolbox/scripts/sct_extract_metric.py#L218-L262 However, I can't actually see any usage of them in the script itself: https://github.com/spinalcordtoolbox/spinalcordtoolbox/blob/61ed4a71ceca1ad43b1ccffd76ca8c24ec90a1ad/spinalcordtoolbox/scripts/sct_extract_metric.py#L280-L291 I vaguely remember that these options...

From a user on the forum: > When using sct_extract_metrics, what is the preferred way to deal with partial volume effects in the slice direction for slices and/or per-level data?...

Improve SCT's web presence (e.g. in Google search results)

6

When Googling "spinal cord toolbox", the first result is https://spinalcordtoolbox.com/. (Great!) However, it looks like this:  There's no favicon or summary description, and the website name is "Spinal cord...

Part of investigation for https://github.com/spinalcordtoolbox/spinalcordtoolbox/issues/4085. Command: ``` sct_register_to_template -i sub-errsm37_T1w.nii.gz -s sub-errsm37_T1w_seg_cropz.nii.gz -lspinal sub-errsm37_T1w_labels-vertbody-automatic-keep-1-to-11.nii.gz -c t1 -qc qc -r 0 -ofolder cropped_all-labels_vertbody ``` Traceback: ``` Traceback (most recent call last):...

Unintuitive `IndexError` during C2-C3 detection when using cropped spinal cord segmentation

1

While investigating #4085, I wanted to use `sct_label_vertebrae` to compare SCT-generated labels (vert body) with the existing manual labels (posterior tip of disc), to see how label positioning can affect...

Nibabel headers have methods called `set_sform` and `set_qform`. SCT uses these methods in places like reorientation: https://github.com/spinalcordtoolbox/spinalcordtoolbox/blob/922b8091319051f66d140baf56d2bd0e1ba0a6e8/spinalcordtoolbox/image.py#L1116-L1117 However, in the above example, since we specify `affine` but _don't_ specify `code`,...

Centralize metric-related modules in a new `metrics` submodule

1

_Originally posted by @joshuacwnewton in https://github.com/spinalcordtoolbox/spinalcordtoolbox/pull/3977#discussion_r1087918848_ > This is just a rough idea, and not a solid suggestion, but... > > Thinking about API organization, I'm wondering if we've developed...