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Diffusion Tensor Imaging: The Nitty Gritty

Diffusion Tensor Imaging: The Nitty Gritty. Brought to you by: Meenal and Erica November 2, 2010. Terms. FA: Fractional Anisotropy The eccentricity of the ellipsoid MD: Mean Diffusivity The mean of the three principle eigenvectors

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Diffusion Tensor Imaging: The Nitty Gritty

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  1. Diffusion Tensor Imaging: The Nitty Gritty Brought to you by: Meenal and Erica November 2, 2010

  2. Terms • FA: Fractional Anisotropy • The eccentricity of the ellipsoid • MD: Mean Diffusivity • The mean of the three principle eigenvectors • DTI Terminology Reference: http://ccn.ucla.edu/~jbrown/dti.html

  3. DTI Step 1: Convert Your Data • Convert the DTI DICOM files to NIFTI format

  4. DTI Step 1.A • Change your FSL Output Type • Cd: /usr/local/fsl-4.1.4/etc/fslconf • Run: sudonanofsl.csh • Change FSLOUTPUTTYPE TO NIFTI • Control X • Save? “y” • Relaunch the terminal and check the change

  5. DTI Step 1.B • Edit script as needed • Script: /Volumes/sasquatch/DataManagement/Workspace/Processing/MatlabCode/”MY”Matlab/main_dtipreprocess.m • Make sure your account system preferences are set to /bin/tcsh • Open matlab • Run: main_dtipreprocess.m

  6. DTI Step 2 • Move all folders • done, dti,ec,fsl, medinria, ninfo.txt,reg, vc and vl • From: • /StudyName/Original_Data/nii/subjid/dti • To: • /StudyName/Original_Data/DTI/subjid/dti/

  7. DTI Step 3 • Rename files in: • StudyName/Original_Data/DTI/subj/dti/fsl/ • From: *rec* • To: *$subjID*

  8. DTI Step 4 • Create folders: • Studyname/DTI_Analysis • Studyname/DTI_Analysis/StudyName_MD • Studyname/DTI_Analysis/StudyName_MD/origdata • Studyname/DTI_Analysis/StudyName_FA • Studyname/DTI_Analysis/StudyName_FA/FA

  9. DTI Step 5 • Copy data • Files ending in *FA* • From: StudyName/Original_Data/DTI/subj/dti/fsl • To: Studyname/DTI_Analysis/StudyName_FA/FA • Files ending in *MD* • From: StudyName/Original_Data/DTI/subj/dti/fsl • To: Studyname/DTI_Analysis/StudyName_MD/origdata

  10. DTI Step 6 • Run Tract Based Spacial Statistics using the FSL Package • CD into DTI_Analysis/StudyName_FA/ • Copy dti_tbss1-3.sh • Run script • Note: Errors may occur here if fsl is not set up correctly

  11. TBSS • To Learn More • http://fsl.fmrib.ox.ac.uk/fsl/tbss/ • preprocessing - create FA images from your diffusion study data • tbss_1_preproc - prepare your FA data in your TBSS working directory in the right format • tbss_2_reg - apply nonlinear registration of all FA images into standard space • tbss_3_postreg - create the mean FA image and skeletonise it • tbss_4_prestats - project all subjects' FA data onto the mean FA skeleton • stats (e.g., randomise) - feed the 4D projected FA data into GLM modelling and thresholding in order to find voxels which correlate with your model.

  12. DTI Step 6 • Check mean_FA

  13. DTI Step: 7 • Create sublist in DTI_Documentation • Create folders: • DTI_Analysis/WM2DTI2Template • DTI_Analysis/GM2DTI2Template

  14. DTI Step 8 • Separate mean_FA and mean_MD into gray and white matter • Set up and Run: dti_combined_StudyName.sh • This script: • #Step 1: Reorient the hires to Match the DTI • #Step 2: Create Average Bo • #Step 3: Register hires to Average Bo • #Step 4: Apply warp of hires in DTI space and MD to MNI152 • # Threshold the MD Map > 0 • # Apply the warp (Subject FA to FMRIB_FA template) on MD map • # Step 5: Segment the hires in MNI152 space • # Step 6: Threshold just the WM and GM (Whole-brain) • # Step 9: Multiple registered FA map and mask (WM and GM) • # Step 10: Calculate the Mean FA for WM/ mean MD for WM and GM

  15. DTI Results • Bo+12 directions • FAtarget_WM • MDtarget_WM • MDtarget_GM

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