Do you think s,d of 0.25 is plausible for internal capsule which is an area with dense accumulation of white matter ?

I think it is an accurate reflection if what is in your data. I don't know what your protocol, and hence the precision of your FA estimates, looks like but one could certainly imagine an s.d. like that in an area that is in truth homogeneous if the resulting SNR is poor.

If you are still concerned you can upload IC_FA.nii.gz to http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi and I'll have a look at it.

Jesper

Reza Pakdaman, M.D.
Postdoctoral Fellow
Dept. of Radiology- University of California , San Diego
Radiology Imaging Laboratory
3510 Dunhill St. MC 0852
San Diego, CA 92121
Phone:(858) 822-4404
Fax: (858) 534-6046
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________________________________________
From: FSL - FMRIB's Software Library [[log in to unmask]] On Behalf Of Jesper Andersson [[log in to unmask]]
Sent: Tuesday, June 16, 2009 10:44 AM
To: [log in to unmask]
Subject: Re: [FSL] Hello!

Dear Reza,

We are processing DTI data in our LAB in University of california ,
San Diego with fsl software version 4.1.3 .Currently we are using
fslstats utility of your program. I have noticed a paradox in the
output of the program and hereby want to notify you about it :

I have used the following command on the FA map of the DTI of a
healthy subject processed by fsl :

fslstats 1_FAfsl.nii.gz -m -M -s -S -r -R

The FA values are between 0 and 1 . the results of the program are :

0.050226 0.212998 0.120878 0.165211 0.000000 0.487615
0.000000 1.195134

so in the output the program calculated the range for non-zero
voxels between zero and 1.195 which is not correct at all (0<FA
value <1)

FA values > 1 is a consequence of a negative eigenvalue of the tensor.
It is true that this is something that is "physically" impossible, but
in practice something that is frequently observed with noisy data.
Consider a voxel in an area with little/no signal. The true
eigenvalues should be [0 0 0] (i.e. we have no signal and no
diffusion). However, the estimated eigenvalues will be associated with
some uncertainty e, so you'll really observe [0庸 0庸 0庸], and hence
some of those values will be negative leading to FA>1.

-in the second stage we used the internal capsule , and purely
internal capsule as the ROI and the results are as follows :

-fslstats IC_FA.nii.gz -m -M -s -S -r -R

0.000010 0.607764 0.002601 0.251947 0.565753 0.791101
0.000000 0.793482

So according to the program results the range of data f is 0.56 -
0.79 , the mean for non-zero is 0.607 , however the SD for non-zero
is 0.2519 .It looks completely unacceptable .

0.56 -- 0.79 is the "robust" range, i.e. ignoring the tails of the
observed distribution of values. The full range is 0 -- 0.79, the next
two values. And then an s.d. of 0.25 looks more plausible.

Good Luck Jesper