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DTI pre-processing

DTI pre-processing. Qiang Wang. Movement Disorders and Neuromodulation Unit. 26 .02.201 9. A common preprocessing pipeline for DTI preprocessing. 1. DICOM s to NIfTI s 2. Topup : correcting Susceptibility-induced Distortions

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DTI pre-processing

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  1. DTI pre-processing QiangWang MovementDisordersand NeuromodulationUnit 26.02.2019

  2. AcommonpreprocessingpipelineforDTIpreprocessing 1.DICOMs to NIfTIs 2. Topup:correctingSusceptibility-induced Distortions 3. Eddy:correcting Eddy Currentsdistortions andheadmovement

  3. Topup: Susceptibility-induced Distortions, caused by difference of gradient field; most interfaces between air, bone, and soft tissues, Green: real brain

  4. Eddy Currents: generated by conductive material coils, shields, tubes, wires or devices within or on the patient

  5. tools Dcm2niix:convertDICOMstoNIFTfiles, advantages:1.NiFTsandbvec are compatible with FSL 2.b-vecwill be oriented with respect to the voxels FSL:pre-processing

  6. Diffusion data: • dti.nii(4Dnifts):dti_AP.nii,AnteriorPosterior phase-encoding directionacquisitions. dti_PA.nii,Posterior AnteriorPEacquisitions OrRLandLRacquisitions. • bval:short for b value,is a factor that reflects the strength and timing of the gradients used to generate diffusion-weighted images • bvec:short for b vectors,contains a 3x1 vector for each gradient,x,y,z, indicating the gradient direction. PS:ifnocompletePAacquisitions,additional PA phase-encoded b0imageatleast

  7. b=0 b=1000 b=3000 Brain DWI images using 3 different b-values (0, 1000, and 3000)

  8. dti.nii bval=1000,n=69 Fslinfodti_AP.nii bval=0,n=1 dimension volumes spacing

  9. bval bvec

  10. Topup extracta volume without diffusion weightingfromdti.nii,b0(APPEdirection)andb0(PAPEdirection) 2anacqparams.txt, containing the following rows: -1meansAPdirection,1meansPAdirection,0.075184isreadout time 3.merge the AP(nodif_AP.nii) and PA(nodif_PA.nii) images into a single image 4.topup: fslroidti_APnodif_AP 0 1 fslroidit_PAnodif_PA01 0 -1 0 0.075184 0 1 0 0.075184 fslmerge -t AP_PA_b0 nodifnodif_PA topup --imain=AP_PA_b0 \ --datain=acqparams.txt \ --config=b02b0.cnf \ --out=topup_AP_PA_b0 \ --iout=topup_AP_PA_b0_fout \ --fout=topup_AP_PA_b0_iout (movement between nodif_AP and nodif_PA) (Susceptibilityinformation off-resonance field) (off-resonance field looks like) (unwarped and corrected image)

  11. topup before after

  12. Topup 5.applytopup:apply correcteddistortionby topupforremaining volumes(APor/andPAdirection) applytopup --imain=dti_AP--inindex=1-- datain=acqparams.txt --topup=topup_AP_PA_b0 --out=hifi_dti--method=jac (Correcteddistortionsdti_APacquisition) 0 -1 0 0.075184 0 1 0 0.075184 (APdirection) acqparams.txt (PAdirection) Forexample:imain=dit_PA--,inindex=2--……

  13. applytopup before after hifi_AP.nii(avolume,b=1000) dti_AP.nii(avolume,b=1000)

  14. Eddyforeddycurrentandheadmovement fslmathstopup_AP_PA_b0_iout -Tmeanhifi_nodif (AveragedAPandPAb0acquisitons) 1.average corrected b0 volumes(asatemplate) creatamask(basedonhifi_nodif)toseparatebrainfromnonbrain 2. bet hifi_nodifhifi_nodif_brain-m -f 0.2 3.eddy eddy --imain=dti_AP\ --mask=hifi_nodif_brain_mask\ --index=index.txt\ --acqp=acqparams.txt\ -- bvecs=bvec \ --bvals=bval \ topup=topup_AP_PA_b0 \ - out=eddy_unwarped_images\ -- flm=quadratic \ ---fwhm=0 \ --data_is_shelled index.txt,contains a singlerow of ’1’, each1for each volume in dti_AP

  15. DTIpreprocessing before (dti_AP,b=0) (eddy_unwarped_images,b=0) after

  16. DTIpreprocessing before (dti_AP,b=1000) (eddy_unwarped_images,b=1000) after

  17. Thanksforyourattention!

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