Jan Valosek

We also have to think about how to save this additional information (comments and person doing the QC). The currently used YML format will not be directly compatible with this....

Adding one more tweak command for nerve rootlets segmentation (relevant for [ivadomed/model-spinal-rootlets](https://github.com/ivadomed/model-spinal-rootlets) project). ``` sct_qc -i sub-brnoUhb01_T2w.nii.gz -s sub-brnoUhb01_T2w_seg-manual.nii.gz -d sub-brnoUhb01_T2w_label-rootlet.nii.gz -p sct_deepseg_lesion -plane axial -qc qc -qc-subject sub-brnoUhb01 ```...

Sagittal view of a native image registered to the PAM50 template using `-p sct_image_stitch`: ```console sct_qc -i ${SCT_DIR}/data/PAM50/template/PAM50_t2.nii.gz -s ${SCT_DIR}/data/PAM50/template/PAM50_cord.nii.gz -d anat2template.nii.gz -p sct_image_stitch ``` ![Kapture 2023-10-21 at 10 22...

Sagittal view of a native image registered to the PAM50 template overlaid with `${SCT_DIR}/data/PAM50/template/PAM50_levels.nii.gz` using `-p sct_label_vertebrae`: ```console sct_qc -i anat2template.nii.gz -s ${SCT_DIR}/data/PAM50/template/PAM50_levels.nii.gz -p sct_label_vertebrae ``` ![Kapture 2023-10-21 at 10...

Mid-vertebral levels created using `sct_label_utils`: 1. labels on the labeled segmentation: ```console sct_label_utils -i t2_seg_labeled.nii.gz -vert-body 3,9 -o t2_labels_vert.nii.gz -qc ~/qc_singleSubj ``` 2. labels on the source image (T2w in...

Cross-referring relevant issue about new compression metrics: https://github.com/neuropoly/idea-projects/issues/19

Thanks for your swift digging into this issue, @joshuacwnewton! > So, my question is: Why does the `nnU-Net` software care about the "unused" dim/pixdim fields? This seems overly sensitive to...

After deeper digging, it seems that the nnUNet errors are not caused by `pixdim` how I initially thought: > Notice the difference `2.5, 0.889114, 0.0, 0.0, 0.0` vs `2.499999, 1.0,...

> I have some follow-up questions: Good questions! I don't have the answers right now. We will continue with further digging.

Might be remotely related to https://github.com/ivadomed/model_seg_sci/issues/21. It seems that `torchIO` also uses `SimpleITK`.