Oh, forgot to mention: if/when you have uploaded the data you need to
email me (off the mailbase) the reference number you are given.
J
On 16 Jun 2009, at 21:01, Pakdaman, Reza wrote:
> Do you think s,d of 0.25 is plausible for internal capsule which is
> an area with dense accumulation of white matter ?
>
>
> 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
> [log in to unmask]
> ________________________________________
> 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 [0ħe 0ħe 0ħe], 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
>
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