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Cerebral Blood Flow (CBF) quantification (please specify the model used)

Function name: asl_perf_subtract.m / asl_perf_subtractMB.m

  • Description: For CASL and PASL, generate the difference and calculate the perfusion images from control/label and M0 images
  • Inputs: Please see the description in the MATLAB code for detailed information.
  • Outputs: Will output CBF maps into the path you defined
  • Syntax: One example for PASL quantification. Both P and M0img are paths for control/label and M0 images: FAIR='C:\Users\...\FAIR_CL.nii'. 
    perfnum =  asl_perf_subtract(FAIR,1, 0, 0, [0 0 1 0 0 1 0 1 0 0], ...
                             0.5, 0, 0.9, 1, 2, 0.8, 45, 20, M0img);
perfnum =  asl_perf_subtractMB(FAIR,1, 0, 0, [0 0 1 0 0 1 0 1 0 0], ...
                             0.5, 0, 0.9, 1, 2, 0.8, 45, 20, M0img);

Function name: ASLQuantificationPCASL.m

  • Description: For pCASL, calculate the perfusion maps with difference images, M0 and related parameters according to the 2015 ASL white paper
  • Inputs: data, M0 and mask should be the matrix for pCASL difference, proton density and brain mask images
  • Outputs: Will generate CBF maps in MATLAB workspace
  • Syntax: [output, output_nantmean, NANCOUNTMASK] = ASLQuantificationPCASL(data, M0, 1.8, 1.8,1.6, 0.9, 0.6,'no','',14, 1, mask, 'yes', 'yesfigure');

Notes

This script needs small modification as shown in the script.

Function name: batch_calc_rcbf.m

  • Description: Calculate the normalized perfusion maps divided by the mean flow
  • Inputs: Choose perfusion maps and mask in the pop out windows
  • Outputs: Will generate normalized CBF maps in same path as original CBF maps
  • Syntax: Just run the whole script, no function to call.

Notes

This script seems to be one code from a whole pipeline. Therefore, there is dependency on passing the file path and subjects with spm batch system. But can use the core code lines as a separate function.

Function name: ASLDeltaM.m

  • Description: Calculate the difference images from the control and label images
  • Inputs: CTRL and TAG are matrix values from the control and label images of ASL images, method can be any value as shown in the script
  • Outputs: Output will be a matrix for difference images in MATLAB workspace
  • Syntax: Output=ASLDeltaM(CTRL,TAG,'PairWise');

Function name: batch_perf_subtract.m

  • Description: batch file for the same function as asl_perf_subtract.m

Function name: ASL_calculateCBFmap.m

  • Description: This function obtains CBF value in the unit of ml/100g/min
  • Inputs: path_temp: the paths of the ASL images, asl_paras: the parameters of the ASL images
  • Outputs: a CBF map in .img format is created in the specified path
  • Syntax: ASL_calculateCBFmap(path_temp,asl_paras)

Notes

The images are in .img format, instead of dicom or nifti.