Review of automatic MP2RAGE segmentation

spinal-cord-7t / coil-qc-code

7T Spinal Cord Coil QC Analysis Code

0 stars 0 forks source link

Review of automatic MP2RAGE segmentation #47

Closed jcohenadad closed 2 months ago

jcohenadad commented 2 months ago

After implementing a fix for #22, we need to identify what subjects need a manual segmentation:

TODO:

[x] sub-MPI1
[x] sub-MPI2
[x] sub-NTNU3
[x] Upload labels to OpenNeuro (https://openneuro.org/datasets/ds005025/versions/2.3.0)

jcohenadad commented 2 months ago

sub-MPI1_UNIT1 has no visible contrast between the cord and the CSF, so I'm using sub-MPI1_inv-1_part-mag_MP2RAGE.nii.gz instead, with sct_deepseg:

jcohenadad commented 2 months ago

I wanted to do the same strategy for sub-MPI2 but I ran into #48

I ended up re-doing the segmentation manually