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ASL_RobustNormalization Pipeline

Pipeline: ASL_RobustNormalization

Type: ASL

Description: Applies nonlinear warp field in output of RobustPipeline to ASL maps

Source: Northwestern University

This pipeline takes the nonlinear warp field in the RobustPipeline output to bring ASL maps into template space. Steps include:

1. Locate native space T1 (head.nii), anat2tpl.warp.field.nii, brain.msk.nii, gm.nii and wm.nii within RobustPipeline tar file
2. Locate T1.nii and *qCBF*.nii in ASLpipeline output
3. locate warp.mat (matlab batch file containing coregistration and VBM warping tasks) & replace inputs with above files
4. Co-register ASL T1.nii to head.nii
5. Apply anat2tpl.warp.field.nii to: *qCBF*.nii, brain.msk.nii, gm.nii and wm.nii
6. Threshold wwm.nii to 99% and extract WMCBF in 99% WM.
7. Subtract WMCBF from CBF map, divide by GM fraction to get partial volume correction. (Limit to GM>=0.3 to avoid division by small numbers)
8. Save FOVmask.nii, which is the combination of ASLmap thresholded at CBF>5, brain.msk.nii and GM>=0.3, in ASLpipeline output folder
9. Save CBF_PVc.nii, the partial volume corrected CBF map, in ASLpipeline output folder