Jan Valosek
Jan Valosek
Just for the record, I encountered the same ITK direction error also for `sci-zurich` dataset after using `sct_crop_image` and `sct_resample` (used preprocessing script available [here](https://github.com/ivadomed/model_seg_sci/blob/3a8403004586c5c98bf4c62fb9e2e190cff1fb2f/preprocessing/preprocess_data_sci-zurich.sh)). Again, I fixed the issue...
Thank you for digging into this, @joshuacwnewton! The following two things came to my mind (sorry if they are irrelevant): 1. Resampling: I believe that the most common image resolution...
> Also, FYI, FSLeyes actually supports matplotlib colormaps out of the box! I only discovered this recently, but you can pass the name of an MPL colormap to FSLeyes on...
Could you please also show what the rootlets look like on T2w with the transparent black layer? (i.e., just T2w image without rootlets segmentation). In other words, I am wondering...
> See related discussion: [neuropoly/idea-projects#15 (comment)](https://github.com/neuropoly/idea-projects/issues/15#issuecomment-1400709359) Just for the full context. Here is how the images in [neuropoly/idea-projects#15 (comment)](https://github.com/neuropoly/idea-projects/issues/15#issuecomment-1400709359) were obtained: ``` # Sagittal image # Crop around the middle...
I have just found out that we can already get sagittal centerline QC using this small hack (passing `-p sct_label_vertebrae` instead of `-p sct_get_centerline`): ``` sct_qc -i sub-cal056_ses-M0_T2w.nii.gz -s sub-cal056_ses-M0_T2w_seg_centerline.nii.gz...
Just for the record, `sct_qc -p sct_label_vertebrae` also works well for getting a rough idea of SC seg in the sagittal plane:  Command: ```console...
The newly added spinal cord module was added to week 2 in https://github.com/school-brainhack/school-brainhack.github.io/pull/322. I believe the issue can be closed.
> Tagging TA @valosekj for review :) Nice! I have a vacation from 9-17 June --> will review it after.
Apologies for no review from my side; it somehow slipped through the cracks. Indeed, the project looks good. Thanks for merging!