With the segmentation results from the first 350 subjects, we decided to only use T1w images for the project:
Subjects to correct segmentation
T1w: 15/350
T2w: 50/350
Subjects to exclude→ 47 / 700 from QC report
T1w : 6/350
T2w : 41/350
This implicates that the processing pipeline needs to be adjusted to only generate sc segmentations and vertebral lableing for T1w images (mainly in process_data.sh) .
Tasks
The removal of T2w images implicates the following changes:
[x] Remove T2w processing from process_data.sh
[x] Adapt compute_stats.py to remove T2w from the statistical models
Context
With the segmentation results from the first 350 subjects, we decided to only use T1w images for the project:
This implicates that the processing pipeline needs to be adjusted to only generate sc segmentations and vertebral lableing for T1w images (mainly in process_data.sh) .
Tasks
The removal of T2w images implicates the following changes:
process_data.shcompute_stats.pyto remove T2w from the statistical modelsREADME.mdmainly Data collection and organization