I have to run BET with -F function to remove this problem to generate FA

maps with no 0 intensity voxels, which is not the standard way of doing

BET on DTI data. May I ask again why is it that if I run BET this way
instead of the standard way -f, the resulting FA map will no longer have
0

intensity voxels?

thanks

Siemwin

Dear Siew-Min,

and everyone else concerned with FA<0 or >1.

These values may seem disconcerting because we know that they are

"impossible", i.e. they come from voxels where the diffusion is

negative in some direction (indicating a black hole or some such thing

to which things can diffuse and disappear).

If instead you see it as having some set of data (your raw diffusion

data) affected by measurement error, and from these data you want to

estimate some parameters (let us say the diffusion in some direction).

The true value will be positive (though it can be quite small in the

case of hindered diffusion in white matter), and then our estimate

will have some finite precision that depends on the quality of the

data (SNR, # of directions etc). So, typically we will not calculate

the "true" value, but some value that is drawn from a distribution

around the true value (known as the "sampling distribution").

In some instances the true value is small (i.e. close to zero), and

then the sampling distribution (i.e. values that we may calculate)

will extend across zero. Then there is a chance/risk that we will

calculate/observe a negative diffusion value and subsequently an FA>1.

This might happen e.g. in highly anisotropic areas in the brain.

In other instances there isn't really a meaningful signal (e.g.

outside the brain) and the precision of our estimate will be very

poor, which again means that we may calculate/observe a diffusion < 0.

So, in short. We never get the "true" FA value. We get an estimate,

and that estimate can be more or less wrong (i.e. it can have better

or worse precision). Sometimes these "wrong" values are also

"impossible", but that doesn't really make them any more "wrong". It

just becomes a bit more obvious.

By increasing the quality of our data (higher SNR and/or more

directions) the errors become smaller and smaller, and the chance/risk

of calculating a negative diffusion becomes smaller. But it doesn't go

away. It just becomes so small that it is very unlikely that we

calculate/observe one given that we are only looking at a few tens of

thousands of voxels.

Therefore, I would suggest stop worrying about negative FA<0 or FA>1

and accept them for what they are. Noisy estimates of some unknown

value in the range 0-1.

Good luck Jesper

On 13 Mar 2009, at 15:11, Siew-Min Gan wrote:

Hi all,

     I noticed my FA map output from DTIFIT has white matter brain

voxels of 0 and >1. I ran the following procedures to get the FA

map.

i.eddycorrect on the original DTI

ii.bet the eddycorrected data.nii.gz (or the 1st B0) to derive the

nodif_brain_mask.

iii.feed the nodif_brain_mask, data.nii.gz,bvecs and bvals into

DTIFIT.

If the original data is ok, could a problem with the bvecs file result

some brain voxels with 0 intensity (or intensity>1) in the FA map

output

from the DTIFIT procedure?

Initially, I thought it may be a problem with the original DTI data,

however, it is a standard MGH 30 dir sequence, and the gradient file

is

from the diffusion toolkit.  I ran the data on another DTI software

and

the FA map output doesnt seem to contain 0 intensity voxels, but it

may be

a scaling issue??

The solution I tried with FSL is to do BET using the -F function

(normally

used for 4D FMRI). The resulting FA map from DTIFIT only then will not

contain 0 intensity voxels, but still have voxels of intensity>1. I

notice

this is not the standard way to process (BET) DTI data.

I am concern about this as I have significant positive results from

the

tbss FA voxel analysis. I wonder if these results would be

independent of

the fact that some voxels in the FA maps are >1. Also, I could not

analyse

the tbss using the FA maps from the standard processing pipeline due

to

some brain voxels having 0 intensity.

May I ask if using BET with -F is ok? Has anyone has come across this

problem before, and may explain why there may be voxel with 0

intensity or

intensity>1 in the FA maps output?

Many Thanks for some kind advice.

Siewmin