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

7T Spinal Cord Coil QC Analysis Code
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Make sure extraction does include values interpolated close to zero values #78

Open jcohenadad opened 1 week ago

jcohenadad commented 1 week ago

This code:

https://github.com/spinal-cord-7t/coil-qc-code/blob/83dfd087445fb045dad77d2320847ff4af5492f9/data_processing-phantom.ipynb#L399-L406

is problematic if the previous step registered qMRI maps that contain zero. Linear interpolation was used, which would under-estimate the qMRI values.

Two options to avoid this:

  1. Use NN interpolation, and then extract metrics while ignoring zero values (eg could use a mask)
  2. Do the extraction within the native space using the registered mask (not the other way around). Cons: the coordinate limits will be different for each site.

Option 1 is more preferable.

jcohenadad commented 1 week ago

Checking for sub-MGH_acq-famp_TB1TFL:

sct_apply_transfo -i ../../sub-CRMBM/fmap/mask_spinalcord.nii.gz -d sub-MGH_acq-famp_TB1TFL.nii.gz -w warp_sub-CRMBM_acq-famp_TB1TFL2sub-MGH_acq-famp_TB1TFL.nii.gz -x linear

Looks fine (ie: no zeroed values): image

I checked the other sites, and it looks fine either.

Next step: check for DREAM and SNR, but need to solve https://github.com/spinal-cord-7t/coil-qc-code/issues/79 first