[Mristudio-users] Extract values of the Fiber tract ROI

[susumu]

Dear Users,

Javier raised an important issue and I want to share his results with all of
you.

Here is what he did;

1) Did fiber tracking using DtiStudio, use the "statistics" button, and get
an FA value of the entire reconstructed fiber.
2) Save the fiber tracking results as 1/0 binary image, load the file to
RoiEditor, superimpose the binary masking on the FA map, and get an FA value
of the entire reconstructed fiber

The results were different as indicated in his email.

This is because the ways FA is measured for the reconstructed tracts are
fundamentally different between the two programs.

DtiStudio:

Suppose you have two fibers. One is 10-pixel long and the other is 5-pixel
long. Also suppose that the second 5-pixel fiber shares the same 5 pixels
within the first 10-pixel fiber. This means, the second fiber is completely
contained within the first fiber.

In DtiStudio, FA is measured along the first fiber. It also measures FA
along the second fiber. The end result is, for example;

First fiber [0.2, 0.25, 0.3, 0.35, 0.4, 0.45, 0.5, 0.55, 0.6, 0.65]
Second [0.2, 0.25, 0.3, 0.35, 0.4]

As you can see, the first 5 pixels are identical. Then DtiStudio calculates
the average of the 15 pixels. This means, the first 5 pixels are
"double-counted". 

In this way, DtiStudio provides natural weighting for pixels that contain
more fibers. In reality, some pixels may contains 10s of fibers
(reconstructed streamlines) while some pixels may contain only one fiber.
The more fibers a pixel contains, more weighting it receives, because it
would be counted many more times.

RoiEditor:

Once you save the fiber tracking result into 1/0 binary information, all the
streamline information is lost, so as the number of fibers each pixel
contains. In RoiEditor, the binary image can be read and applied to an FA
map as a non-weighted binary masking. 

I hope this explains the difference among the two methods. Because DtiStudio
counts the core white matter regions many more times than peripheral areas,
the average FA values tend to be higher.

There is nothing like one is better than the other. They are just two
different approaches. Maybe the natural weighting may sound more reasonable
but the non-weighting 1/0 masking should also be a valid approach. You just
need to apply the same method (or both methods) to all data. 

Please let us know if you have any questions regarding this issue.

Thanks,

Susumu



________________________________________
From: Javier Navas [mailto:fjnavas2 at gmail.com] 
Sent: Tuesday, March 17, 2009 6:55 AM
To: susumu at mri.jhu.edu; DTI Studio, ROI Editor, Landmarker Questions/Support
Subject: [Mristudio-users] Extract values of the Fiber tract ROI


Thank you very much Mr. Susumu,

with ROI editor I can extract the pixel values in a txt file, that is what I
want, thank you. 

But I have a problem. The FA mean value that results in DTI Studio is
different that the FA mean value that results in ROI editor, with the same
binary image, why occur this?. 

For example, with the same mask of the genu of corpus callosum, I have the
same number of pixels (2835 pixels) but the FA statistics is different. 

DTI studio: 
      FA
        Max. of ImgVal:   0.9690
        Min. of ImgVal:   0.0591
        Mean of ImgVal:   0.5385
        Std. of ImgVal:   0.1689 

ROI editor:
         Min:    0.06
         Max:    0.97
         Mean:    0.45
         Std:    0.17

________________________________________
From: mristudio-users-bounces at mristudio.org
[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Javier Navas
Sent: Thursday, March 12, 2009 8:33 PM
To: DTI Studio, ROI Editor, Landmarker Questions/Support
Subject: Re: [Mristudio-users] Extract values of the Fiber tract ROI

Hi Susumu,

I`m talking about the statistics of the fiber tracking results as an ROI. I
want to extract all the voxels values in the FA map that are included in the
corpus callusum tract to a text file. I don`t want only the mean or the
max/minimum value. Becouse I want to do a parcellation of the corpus
callosum and do a correlation of this values with the age or the IQ of the
pacients.

I´m working with the software some months ago, and I`m new in the list. This
is my first message. Thank you for your answer.

2009/3/13 susumu <susumu at mri.jhu.edu>
Hi Javier,
 
Are you talking about the statistics of the ROI you drew or using the fiber
tracking results as an ROI?
 
Susumu
 
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________________________________________
From: mristudio-users-bounces at mristudio.org
[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Javier Navas
Sent: Wednesday, March 11, 2009 8:15 AM
To: mristudio-users at mristudio.org
Subject: [Mristudio-users] Extract values of the Fiber tract ROI
 
Dear all,

I`m working in Fiber Tracking of the corpus callosum with DTIstudio,

I want to extract the values of my ROI (the statistics with the number of
fibers selected, length of fibers, FA values...) to a text file or SPSS
archive, but I don`t know how can I do it.


Thank you for help me,

Javier 

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