[Mrtrix-discussion] FA and ADC values for a tract

[Thijs Dhollander]

Hi Helen,

Opinions on FA/ADC quantification can be wildly varying... :-)  There's no
problem calculating and reporting their values, but interpretation is a big
issue: they can be quite sensitive in many cases, but they are always far
from specific.  To avoid starting a long rant on how we should abandon
these measures as quickly as possible, I'd rather refer to this nice
article: http://www.sciencedirect.com/science/article/pii/S1053811912007306;
it contains some nice and clear passages explaining some of the
relevant
issues to be wary of, as well as further references that are worth a good
read.
So the question remains: what's better then?  There's quite some
alternatives, but I personally particularly like apparent fibre density
(AFD).  A nice and in-depth article on it can be found here:
http://www.sciencedirect.com/science/article/pii/S1053811911012092 .  Last
year's ISMRM had an abstract on some further improvements on analysing AFD:
http://cds.ismrm.org/protected/13MPresentations/abstracts/0841.pdf (if you
or anyone in your lab attended, they can access it;  the accompanying oral
presentation can be found at
http://cds.ismrm.org/protected/13MPresentations/0841/ ).  The next big
version of MRtrix (expected to be released somewhere around this year's
ISMRM in May... ;-)) will contain much more tools that provide you with the
means to perform such analyses.
In the mean time, you can already easily obtain an (orientationally
averaged) AFD map by simply calculating the average of your (normalized)
DWI images from a single shell acquisition.  The same contrast (up to a
fixed constant factor) can also be obtained by opening up the result from
an SH fit of the signal (or even a CSD outcome) in mrview, and looking at
the first coefficient (i.e. the 0th order).

Hope this already helps somewhat!

Cheers,
Thijs

PS: now that I've mentioned the upcoming ISMRM; I'd like to encourage
everyone on this list that still has many questions (or not) to surely
attend and look for each other -- discussions on these new and better ways
of quantifying are always much more lively in person :-)



*Thijs Dhollanderthijs.dhollander at gmail.com <thijs.dhollander at gmail.com>
Tel. +32 475 36 44 27*
Medical Image Computing (MIC), ESAT-PSI, Department of Electrical
Engineering, KU Leuven


On Wed, Mar 26, 2014 at 4:52 PM, Helen Carlson <
Helen.Carlson at albertahealthservices.ca> wrote:

> Hello Thijs
>
> Thank-you for your reply to my question. I would like to quantify changes
> in white matter over time, specifically pre/post treatment. Is there a
> better way to do this than using the mean FA and ADC? Or is this
> measurement appropriate?
>
> Thanks again
>
> Helen.
>
>
>
> *From:* mrtrix-discussion-bounces at www.nitrc.org [mailto:
> mrtrix-discussion-bounces at www.nitrc.org] *On Behalf Of *Thijs Dhollander
> *Sent:* March 23, 2014 9:47
> *To:* mrtrix-discussion at www.nitrc.org
> *Subject:* Re: [Mrtrix-discussion] FA and ADC values for a tract
>
>
>
> Hi Helen,
>
> What you're seeing is (probably) correct: FAs larger than 1 and ADCs below
> 0 can appear due to the tensor estimation in MRtrix being a simple
> (unconstrained) linear least squares one.  The tensors are not explicitely
> constrained to be positive definite, and thus negative eigenvalues might
> appear.  When one or more eigenvalues of a given tensor are negative, the
> FA can go beyond 1, while the ADC can go below 0.
>
> Cheers,
> Thijs
>
>
>
>
> *Thijs Dhollander thijs.dhollander at gmail.com
> <thijs.dhollander at gmail.com>Tel. +32 475 36 44 27*
> Medical Image Computing (MIC), ESAT-PSI, Department of Electrical
> Engineering, KU Leuven
>
>
>
> On Fri, Mar 21, 2014 at 10:10 PM, Helen Carlson <
> Helen.Carlson at albertahealthservices.ca> wrote:
>
> Hello all,
>
> I would like to determine the average FA and ADC values for a given track
> (in this case, the arcuate). So I followed previous directions posted here
> and have used the following commands on my arcuate which successfully
> creates a probability mask for FA and ADC:
>
>
>
> tracks2prob -template fa.mif Arcuate.tck FA_mask.mif
>
> tracks2prob -template adc.mif Arcuate.tck ADC_mask.mif
>
>
>
> I then used mrstats to get the average, max, min etc of the tracks by
> using these commands:
>
>
>
> mrstats fa.mif -mask FA_mask.mif
>
> mrstats adc.mif -mask ADC_mask.mif
>
>
>
> Which also seemed to work except that I was expecting my FA to range from
> 0.1 to 1.0 (approximately). Instead, the FA values have a min of 0 and a
> max of 1.13. In addition, my ADC values have a negative minimum (-0.0024).
> It seems these values are out of range and do not make sense but I do not
> know what I am doing wrong.
>
>
>
> Thanks in advance for any help
>
> Helen
>
>
>
>
>
> *Helen Carlson, Ph.D*
>
> Neuroimaging Research Associate
>
> Calgary Pediatric Stroke Program & Neuropsychology
>
> Alberta Children's Hospital
>
>
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