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
modulateThis 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.

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