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

[Helen Carlson]

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<mailto: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<mailto: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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