DTI Analysis

DTI Analysis

Processing Data with FSL's FDT Diffusion

When you collect data, you need to turn the gradients on to their maximum value. But this also puts eddy currents into the scanner causing distortion. So when you go to calculate the FA, the images aren’t always in the right place (motion). You must use the motion correction feature.

1. Start FSL (click on the FSL icon, or launch Cygwin and type 'FSL' from the command line).

2. Press the FDT Diffusion button to show the diffusion processing window. 3. At the top, select the EDDY CURRENT CORRECTION.

1. It asks for the data file, which is filename_data.hdr.

2. Also, put in the output name you want to identify it as the corrected data. Filename_data_cor

3. The reference volume is 0 (back to b-value of 0).

4. Press 'Go' to run the Eddy Current Correction and wait for it to complete before progressing to the next step.

5. Now, select DTIFIT RECONSTRUCT DIFFUSION TENSOR. at the top

1. This will take diffusion images and directions, and calculate the tensor for each point in the mask and give results. FSL assumes 1 data set, but it needs others, so click on SPECIFCY FILES MANUALLY. 2. Diffusion weighted data This is your corrected file. (Filename_data_cor)

3. BET Binary map you have to make this using BET in FSL.

1. Press the 'BET' button from the main FSL window 2. Input is your corrected data file again.

3. Under ADVANCED OPTIONS, check GENERATE BINARY MASK.

4. The Fractional Intensity Threshold should equal 0.3.

5. Uncheck Generate image with non-brain matter removed. 6. Select OK.

7. So now, put the name of your brain mask image into the 'BET Binary map' box.

4. Gradient directions - choose _bvec file. 5. B-Values - choose _bvals file.

6. 'Go' to run the DTI fit and wait for it to complete before progressing to the next step.

o NOTE: Make sure your output name is clear and unique and that all pathways are written correctly.

o You will get an error message, but just ignore them. Vieiwing DTI data withe FSLview

FSL has written the results as analyze format files, and you can open then in FSL

View. Your files should be saved in your data folder. It will save one file with the title 'FA', which refers to the Fractional Anistropy map. It also saves the three orthogonal vectors (V1, V2, V3).

1. Start FSL (click on the FSL icon, or launch Cygwin and type 'FSL' from the command line).

2. Press the FSLview button.

3. Choose File/Open and select the FA map.

4. Choose File/Add to add an overlay - select the V1 file to show principle vectors.

5. In box on the bottom, you can see what you have loaded (FA and V1); to turn the overlay off, just click on the eyeball.

1. Select the info button (i with circle) after highlighting V1. 2. Overlay Information: Greyscale 3. DTI Display: LINES.

In FSL View, you can scroll at each axis, move crosshairs (+), move stuff with hand, and zoom with big box/little box, just click and drag. You can add lots of files as overlays. The L1, 2, and 3 are your eigenvalues, MD is the ADC value (mean

diffusivity), and your eigenvectors are V1, 2, and 3 (along and perpendicular to filter if present). If you zoom in, you can see the direction with the slashes. You really only care about where its brighter/higher anisotropy). The typical display seen in papers has the colors.

1. Start FSL (click on the FSL icon, or launch Cygwin and type 'FSL' from the command line).

2. Press the FSLview button.

3. Choose File/Open and select the FA map.

4. Choose File/Add to add an overlay - select the V1 file to show principle vectors.

5. In box on the bottom, you can see what you have loaded (FA and V1); to turn the overlay off, just click on the eyeball.

1. Select the info button (i with circle) after highlighting V1. 2. Overlay Information:RGB

3. DTI Display: Modulate.

FA is grayscale, so FA doesn’t include direction information. Dark is isotropic (same in all directions). Light is anisotropic. Color codes to give directions: Red is left to right. Green is front to back. Blue is head to foot. But this isn’t tractography. Open BEDPOST/ProbTrack This measures the probability of one thing being connected to another. (kind of tracking). It’s good to look at colors in FSL View to be sure everything is done right. Most likely problem is that directions are off.

Tractography with MedINRIA:

MedINRIA is a powerful tractography program. It not only generates lovely images, but also allows measurements of connectivity between regions of interest.

Furthermore, it is easy to use and comes with a good manual. Therefore, this web page only gives a brief description. To proceed, you will need a copy of the

MedINRIA software . The following information assumes you are using version 1.5.2 or later: earlier versions can not read FSL format Bvec files or FSL format .nii.gz files.

To proceed, you need a DTI dataset in NIfTI format and a FSL format BVec file. If your images are from a Siemens scanner, my dcm2nii software will create these for you. The output from FSL's eddy current correction is ideal (see the previous section). 1. Launch MedINRIA 'DTI Track' module by clicking on its desktop icon (or if you have launched the basic MedINRIA, choose 'DTI Track' from the 'Modules' menu).

2. Choose the DTITrack/DTIStudy/New command to describe a new study. A wizard starts, press next.

o Press the 'Open' button and select all your DTI images (e.g. the eddy current corrected 4D image you created with FSL, Filename_data_cor.nii.gz).

o Press the 'Load Sequence' button and select your diffusion direction file (if you used dcm2nii, this will be called *.bvec). o Press Next

3. You will be asked if the orientation is correct, press 'next' and then choose to 'Save' your description: this will create a *.dts file that you can double-click in the future to view, without going through the Wizard. You are now done with the Wizard.

4. You will be asked if the orientation is correct, press 'next' and then choose to 'Save' your description: this will create a *.dts file that you can double-click in the future to view, without going through the Wizard. You are now done with the Wizard.

5. Choose DTITrack/Processing/ComputeFibers to generate your tensors (this will take a few minutes).

6. By default, medINRIA generates a huge fiber tracking region. As shown in the image below, select the control handles (the balls) and reduce the size of your tracking origin (this will make the changes much quicker. You can now reposition the region by moving the center ball.

7. I like adjusting the 'Fiber settings' on the right side of the program to \"3D Ribbons\" with a large radius.

Tractography with DTIStudio:

This software is a good tool to get a quick view of where tracts are. The directions

below are for the Philips PAR/REC files, but you can also use DICOM images. 1. Start DTIstudio

2. Select DTI Mapping and choose 'Open Philips REC'.

3. We have to add all of the Philips REC files to Philips REC Image file(s) box: Load in filename_1.rec for the raw data (remember, _2 and _3 are post-processed).

4. Open MRIcro. Drag the PAR file you want to load it into MRIcro. You have to type in the parameters from MRIcro into DTIStudio. (Use Ctrl+D in

MRIcro to view the PAR file header, or select Import/DisplayForeignHeader). 1. Slice by Slice 2. Z=# of slices.

3. Slices to be processed: all slices 4. Axial slices

5. Inferior/superior (drag through to be sure) 6. FOV = Width x dimension times size 7. Length y dimension times size 8. Slice thickness =2 9. B-value = 1000

5. Gradient Table: Enter in gradients with correct (+) and (-) values. See http://www.mri.jhmi.edu/~craig/protocols/dti.html F.M. Kirby Center - Diffusion Tensor Imaging Protocol – this Java Applet will compute the gradient table

1. Slice Orientation: Transverse 2. Head Feet: Head first 3. Laying: Supine 4. Foldover: AP

5. Fat shift: P(Foldover and fat shift found on scanner in geometry) 6. Gradient Resolution: high is 32, medium is 15, low is 6

7. Gradient Overplus: Yes 8. AP Rotation: 0 9. FH: 0

10. RL: 0AP/FH/RL: Angulation midslice in PAR file. 11. Click Create Gradient Table

12. Note: xyz of image may not be same as scanner.

13. Copy and paste the gradient table output into the table in DTIStudio. 14. Click OK.

6. This will give you MRIView3D file: gives you 3 orthogonal places and 3D view in box.

7. To move it around, click on the line and drag. Use these to judge if everything looks correct.

8. On Right, in Viewer:

1. Image: 2. ROI: no

3. DTI Map: Calculate: Tensor, Color Map, etc.

4. DTI Map Options:Background noise level = 20The rest can stay as the default value. This will display the ADC).

9. Back to Image: select COLOR MAP – 0 10. Save as…

11. Make sure the colors are right because that means the directions are right. 12. Select DTI MAP again, choose Fiber Tracking. The default parameters ok, so you can use the defaults. 13. Select FIBER tab.

14. Draw ROI. All points in ROI are used as start points of fibers.

15. Under fiber selection, check ROI Drawing Enable. Draw around place and double click to finish. Unclick ROI Drawing button.

16. Rotate 3D image to see all fibers that come from your ROI. Remember that the colors are random here.

17. To calculate statistics of a particular ROI, highlight and click statistics. Look at average ADC value and FA value. You could also correlate it with some other variable.

18. Switch back to Tensor Trace in Image. Then back to FIBER. Under Fiber Display, check show fibers in 2D.

Other tools for DTI Tractography

Here are a couple of additional tools for DTI processing.

mrDiffusion can allow viewing as well as powerful statistics. Denis Ducreux's DPTools.

In addition to MedINRIA, Pierre Fillard has created other diffusion processing programs.

• BLOX is a visualization program for use on brain MR, DTI and MRS data. • Volume-One can visualize DTI images.

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Statisitcal Analysis of DTI

By testing a group of people, we can examine whether differences measured by DTI correlate with behavioral performance. To do this, we need to register each

individual's brain to a standard space (normalization) and then conduct voxelwise statistical analysis. Currently, we analyze the FA maps and the MD maps. Using SPM and our own NPM software.