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valosekj committed Sep 18, 2024
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Expand Up @@ -6,7 +6,7 @@ Steps:
1. DICOM to NIfTI (BIDS) conversion
2. Processing (spinal cord and lesion segmentation, vertebral labeling)
3. Quality control (QC) + manual compression level labeling
4. Lesion metric computation
4. Lesion metric computation -- not implemented yet

## Table of contents
- [1. Getting Started](#1-getting-started)
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## 3. Analysis pipeline

The whole analysis pipeline is implemented in the `process_data.sh` script.
The entire analysis pipeline is orchestrated by the `process_data.sh` script.

The script first converts DICOM files to NIfTI (BIDS) format using `dcm2niix`.
Then, it processes the data using SCT functions. After running the SCT functions, the script opens FSLeyes to allow the
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