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

7T Spinal Cord Coil QC Analysis Code
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Generate manual disc labels #27

Closed jcohenadad closed 5 months ago

jcohenadad commented 5 months ago

Write up a procedure with manual-correction to generate the disc labels.

Related to #23

  1. Install https://github.com/spinalcordtoolbox/manual-correction
  2. Download and unzip this config file: config_labels.yml.zip
  3. Run (adapt path): 
    python ~/code/manual-correction/manual_correction.py -path-img data -path-out data/derivatives/labels -config config_labels.yml

This generated the following derivatives labels.zip, which need to be placed under the derivatives/ folder of the input data for subsequent analysis.

TODO:

@NathanMolinier: tagging you so you are aware of another dataset (MP2RAGE UNI) with disc labels

evaalonsoortiz commented 5 months ago

The code no longer runs vertebral labeling, was the removal of that intentional?

jcohenadad commented 5 months ago

The code no longer runs vertebral labeling, was the removal of that intentional?

yes, motivated by https://github.com/spinal-cord-7t/coil-qc-code/issues/23

jcohenadad commented 5 months ago

Second round of labels, using this YAML: config_labels 2.yml.zip

QC: qc_corr_20240423155512.zip

Generated labels (includes previous labels as well): derivatives.zip

jcohenadad commented 5 months ago

Fixed in https://openneuro.org/datasets/ds005025/versions/2.3.1