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

7T Spinal Cord Coil QC Analysis Code
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Generate approximate mask of spinal cord #76

Closed jcohenadad closed 3 months ago

jcohenadad commented 3 months ago

Method to generate approximate spinal cord is illustrated below:

Screenshot 2024-06-08 at 11 13 37 PM

The source of the figure is available here: phantom_mask_creation.zip

Fixes #71

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evaalonsoortiz commented 3 months ago

Looks good. I've pushed some changes : https://github.com/spinal-cord-7t/coil-qc-code/commit/6550f393643c09088c4d4249aa964c4064ee5883 after which I will merge.

evaalonsoortiz commented 3 months ago

After merging this PR I picked up an error. The code starting here: https://github.com/spinal-cord-7t/coil-qc-code/blob/5a5786bd7efa9d39fbfaeb0f2f8076fab2587732/data_processing-phantom.ipynb#L328

assumes that {subject_ref}_acq-famp_TB1TFL_label.nii.gz already exists, but it hasn't been created.

evaalonsoortiz commented 3 months ago

The problem is now fixed in: https://github.com/spinal-cord-7t/coil-qc-code/commit/d9efe5843f2089d277e6197f0de54307378ac173

jcohenadad commented 3 months ago

After merging this PR I picked up an error. The code starting here:

great catch! thank you for fixing this