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

7T Spinal Cord Coil QC Analysis Code
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RuntimeError: ../../sub-CRMBM/fmap/mask_spinalcord_DREAM.nii.gz does not exist #79

Closed jcohenadad closed 3 months ago

jcohenadad commented 3 months ago

Using version d1f8ea06cf20d9a39a57982a72735bcd9136dea2

Indeed, masks for DREAM and SNR used in the code below are not created before:

https://github.com/spinal-cord-7t/coil-qc-code/blob/83dfd087445fb045dad77d2320847ff4af5492f9/data_processing-phantom.ipynb#L401-L402

jcohenadad commented 3 months ago

Two possible solutions:

  1. register the DREAM and SNR to the TFL and use a single mask for all three metrics.
    • pros: faster, less code
    • cons: DREAM and SNR have very different coverage
  2. create separate ROIs
    • cons: introduces a bias when comparing TFL vs. DREAM (ie: we should be comparing using the same mask)

I would go with option 1

@evaalonsoortiz what did you have in mind for this?

evaalonsoortiz commented 3 months ago

I had already co-registered the TFL spinal cord mask to the DREAM and SNR spaces via the command line, and I must have forgotten to add the line of code to the notebook. This way you use the same mask, but don't have the different coverage problem.

Unfortunately, I don't remember the exact line of code that I used, but this seems to have reproduced the masks I had: https://github.com/spinal-cord-7t/coil-qc-code/blob/d2bc792c5388e0d31b4008ca177741a2d7a0f590/data_processing-phantom.ipynb#L359-L364

jcohenadad commented 3 months ago

Change implemented in 6365e3e06f1410d31f5b2e926362791e9272d8b9