Importing NIfTI data

Importing .nii volumes

The following code snippet shows how to import image from NIfTI format to planC.

    % Define location of nii file to import and the the location to save the resulting planC.
    niiScanFileName = 'Path\to\niiFile\FileName.nii'; 
    plancSaveName = 'Path\to\save\cerr_planc.mat';   
    scanName = 'CT';
    planC = nii2cerr(niiScanFileName,scanName);
    % Save planC
    planC = save_planC(planC,[],'passed',plancSaveName);

Importing .nii masks

The following code snippet shows how to import labels mask from NIfTI format to planC.

    % Define the location of nii file containing label mask
    niiMaskFileName = 'Path\to\niiMaskFile\MaskFileName.nii';  
    % Define the scan index in planC to associate the labels/structures.
    scanNum = 1; 
    planC = importNiftiSegToPlanC(planC,niiSegFileName,scanNum);

Changing structure names after importing nii labels

The labels from nii masks are named as ROI_* in planC. The last structure in planC is the union of all the labels in nii file. The following code snippet shows how to change structure names and to delete the combined ROI.

    % Define label to name mapping
    labelToNameC{1} = 'Lung_left';
    labelToNameC{2} = 'Lung_right';
    labelToNameC{3} = 'Heart';
    labelToNameC{4} = 'Esophagus';
    labelToNameC{5} = 'Spinal_cord';

    indexS = planC{end};

    % Delete the combined ROI, the last structure in planC
    numStructs = length(planC{indexS.structures});
    planC = deleteStructure(planC,numStructs);

    % Rename ROIs
    for iStr = 1:length(labelToNameC)
        planC{indexS.structures}(iStr).structureName = labelToNameC{iStr};
    end