SpineReports

Automated extraction of spinal morphometrics and generation of structured radiological reports from MRI data.

How to install ?

1. Open a bash terminal in the directory where you want to work.

2. Create and activate a virtual environment using python >=3.10 (highly recommended):

   • venv

   python3 -m venv venv
   source venv/bin/activate

   • conda env

   conda create -n myenv python=3.10
   conda activate myenv
   

3. Install TotalSpineSeg: see information here

4. Install SpineReports:

   git clone [email protected]:ivadomed/SpineReports.git
   cd SpineReports
   pip install .

How to generate the reports ?

1. Regroup all niftii files into a folder

They need to follow the BIDS naming convention (i.e. sub-<participant_label>_<contrast>.nii.gz)

INPUT_FOLDER/
    subject1_T1w.nii.gz
    subject2_T2w.nii.gz
    subject3_T2w.nii.gz
    subject7_T2w.nii.gz
    ...

2. Run TotalSpineSeg to get generate the segmentations in the 1mm isotropic space

totalspineseg -i INPUT_FOLDER -o OUTPUT_FOLDER --iso

3. Run SpineReports to generate the reports