Create analysis script - Githubissues

sct-pipeline / spine-park

Pipeline for multicontrast analysis in PD patients

MIT License

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Create analysis script #6

Closed jcohenadad closed 8 months ago

jcohenadad commented 9 months ago

The processing script should do the following:

T2w

Segment cord on T2w (0.8mm iso)
Label vertebrae on T2w
Register to PAM50 template
Compute CSA between C2-T5 (average per level)

MTS

Segment cord on mt-on_MTS
Register to T2w using spinal cord segmentation
Register to PAM50 via T2w registration
Register mt-off to mt-on
Compute MTR between C2-T5 (average per level) within various tracts/regions

MP2RAGE

Segment cord on UNI
Register to T2w using spinal cord segmentation
Register to PAM50 via T2w registration
Compute T1 between C2-T5 (average per level) within various tracts/regions

DWI (for each DWI slab):

Average DWI scans
Segment spinal cord on mean DWI scan
Create mask
Motion correction
Average DWI scan
Segment spinal cord on mean DWI_moco scan
Register to PAM50 via T2w registration
Compute DTI metrics for all slices within various tracts/regions

DWI merging of slabs:

Create a script that will combine the three CSV files (one per slab, with some overlap) and that will average the DTI metrics within each vertebral level that exists across the three CSV files.