Closed uzaymacar closed 1 year ago
Here is a visualization of this current preprocessing pipeline for subject sub-amu01
:
The latest commit 957debf dilates the GT mask and crops the images as discussed last week. Data exploration shows that after cropping via the current preprocessing script in this PR and resampling to 1 mm^3:
(44, 102, 278)
(38, 176, 248)
(29, 30, 120)
We'll use these values to inform the selection of center-crop, length, and stride parameters.
NOTE: This PR will NOT be merged and we'll incorporate the preprocessing done here in a unified preprocessing script.
The added script
get_sc_roi_via_centerline.sh
extracts the spinal cord ROI via centerline estimation using SCT'ssct_get_centerline
command.To run this preprocessing, use:
To-dos: