Julien Cohen-Adad

FileNotFoundError: when using `type=im` with `algo=centermassrot`

6

### Description While working on a [forum issue](https://forum.spinalcordmri.org/t/anatomical-registration-between-sessions/957/6?u=jcohenadad), I tried using centermassrot with `type=im` and got the following error: Terminal output ```console sct_register_multimodal -i sub-CTS05_ses-SPpost_T2w_crop_08iso.nii.gz -iseg sub-CTS05_ses-SPpost_T2w_deepseg_08iso.nii.gz -ilabel sub-CTS05_ses-SPpost_T2w_deepseg_labeled_commonverts_prepost.nii.gz -d...

Is `line_angle()` still available in QC for looking at HOG performance?

2

While working on a [user issue](spinalcordtoolbox.reports.qc.QcImage.line_angle()) related to the co-registration of images, accounting for rotation about the S-I axis, i wanted to QC some of the `algo=centermassrot` output based on...

### Description While working on https://github.com/spinalcordtoolbox/spinalcordtoolbox/pull/4533 I stumbled upon potential refactoring. This code: https://github.com/spinalcordtoolbox/spinalcordtoolbox/blob/65ffa7524dc145a23086127be6d9f03ccc6b0778/spinalcordtoolbox/scripts/sct_register_to_template.py#L590-L605 Can re-use the `label` feature of `sct_apply_transfo`: https://github.com/spinalcordtoolbox/spinalcordtoolbox/blob/65ffa7524dc145a23086127be6d9f03ccc6b0778/spinalcordtoolbox/scripts/sct_apply_transfo.py#L200-L206 Instead of re-implementing it. > [!WARNING] > Note...

Add entry `-p sct_deepseg`

2

However, given that there are multiple models in deepseg, this feature will not be straightforward. It will be part of the major refactoring. I'm just opening the issue for prosperity,...

after https://github.com/ivadomed/model_seg_ms_mp2rage/pull/82 is merged, model URL should be updated

Related: - https://forum.spinalcordmri.org/t/anatomical-registration-between-sessions/957/8?u=jcohenadad - #4520 - https://github.com/spinalcordtoolbox/spinalcordtoolbox/issues/1515 - https://github.com/spinalcordtoolbox/spinalcordtoolbox/issues/1464 - https://github.com/spinalcordtoolbox/spinalcordtoolbox/issues/1178 - https://github.com/spinalcordtoolbox/spinalcordtoolbox/issues/978 - https://github.com/spinalcordtoolbox/spinalcordtoolbox/issues/836 - https://github.com/spinalcordtoolbox/spinalcordtoolbox/issues/811 - https://github.com/spinalcordtoolbox/spinalcordtoolbox/issues/666 Data: `duke:projects/sct_zrotation`

When cropping for faster processing, like here for example: https://github.com/spinalcordtoolbox/spinalcordtoolbox/blob/bb479d82ea1e2076dd50343177056a61bd17e260/batch_processing.sh#L136-L139 We can now skip the mask creation (which purpose is simply to dilate the cord segmentation) and instead replace it...

We have a procedure to project disc labels onto the centerline, but the projection is done within the XY plane. It would be much better to instead do the projection...

Develop new method to register odd and even chunks on 3D volumes

3

When 3D volumes are acquired using 2D sequence in an interleaved mode (0,2,4,6,...,1,3,5,7,...), there could be strong motion between the odd and even stacks, as illustrated here:  An idea...

Versioning strategy for Shimming Toolbox

12

### Context Shimming Toolbox is set up between 2 repos - [Shimming Toolbox](https://github.com/shimming-toolbox/shimming-toolbox) - [FSLeyes plugin](https://github.com/shimming-toolbox/fsleyes-plugin-shimming-toolbox) Currently, a user downloads the main branch of the plugin and runs the plugin...