Measuring Background Parenchymal Enhancement (BPE) on MRI - cerr/CERR GitHub Wiki

Software requirements

• CERR
• Plastimatch

User inputs

  1. CERR-format files with the following sequences in order:

    • T1 Non-fat-saturated
    • T1 Fat-saturated (pre-contrast)
    • T1 Fat-saturated (post-contrast)

  2. Matlab table containing pt IDs and laterality information

Running the analysis

1. Segmenting the left and right breasts

fpath = 'path\to\CERR_files';
batchBoundingBox(fpath);

Resulting structures 'Auto_bbox_right' and 'Auto_bbox_left' are saved to the CERR files.

2. Segmenting the FGT

fpath = 'path\to\CERR_files';
latPath= 'Path\to\laterality_table';
outPath = 'Path\to\output\Dir';
batchBPE(fpath,latPath,outPath);

Resulting FGT segmentations associated with the fat-saturated (pre contrast) scan are saved to the CERR files.

3. Computing the FGT ratio, pre- and post-contrast histograms

latPath= 'Path\to\laterality_table';
outPath = 'Path\to\output\Dir';
batchSpreadsheet(outPath,latPath);