[Mristudio-users] Extract values of the Fiber tract ROI
vikey.han
vikey.han at 163.com
Thu Mar 19 10:23:58 EDT 2009
Hi,Susumu, thank you, I learned more from you, then is my following description correct?
if we have two hypothetical “real” tracts with
Fiber1={pixel1,pixel2,pixel3,pixel4,pixel5}
Fiber2={pixel1,pixel2,pixel3,pixel6,pixel7}
generally, the value of FA at pixel3 will be decreased because it is a cross point, so, it is possible that the value of FA at pixel3 is less than the threshold, in this case, we will not track to pixel 3 from the seed point, pixel5, thus will generate three parts:
streamline1={pixel1,pixel2,pixel3} , seeding from pixel 1 or 2 or 3
streamline2={pixel4,pixel5} seeding from pixel 4 or 5
streamline3={pixel6,pixe7} seeding from pixel 6 or 7
furthermore, if we slelect seed, pixel 1, the principal diffusion direction at the pixel 1 maybe change too much so as to more than the threshold of angle.
Is the above correct?
2009-03-19，susumu <susumu at mri.jhu.edu>：
I’m not sure if I understood your question correctly, but let me try.
In DtiStudio, fiber tracking is initiated from all pixels in the brain (more precisely pixels with FA above the threshold). Some may think that tracking is initiated from pixels in ROIs, but that is not the case. We draw ROIs just to retrieve fiber tracking results that penetrate the ROIs.
For the first case of your fibers, ROI could be Pixel2 and for the Fiber #1, the seed pixel could be Pixel#5 and for the Fiber #2, the seed pixel could be Pixel#7. So, it’s possible.
The Case 2 and Case 3 seem not possible because there is no common pixel as your ROI location.
Also, suppose we have hypothetical “real” tract with Fiber1={pixel1,pixel2,pixel3,pixel4,pixel5}
Then we may get 5 streamlines after fiber tracking; one seeded from Pixel#1, one from Pixel#2,,,, one from Pixel#5. These 5 streamlines have slightly different coordinates because each tracking starts from the center of each pixel and tracking takes place in floating number coordinates. For quantification, the streamline information is often converted to pixel-by-pixel information. After this conversion, the 5 floating-point streamlines may converted to the identical string of pixels, which is in this case, Fiber1={pixel1,pixel2,pixel3,pixel4,pixel5}.
In reality, these 5 streamlines often start to diverge at the peripheral regions while the core areas are likely to share many pixels.
From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of vikey.han
Sent: Thursday, March 19, 2009 6:00 AM
To: DTI Studio ROI Editor Landmarker Questions/Support
Subject: Re: [Mristudio-users] Extract values of the Fiber tract ROI
Then I have a question, if the two or more fibers share the same sequence of pixels, how does DTIsutio represent the fibers tracked, for example,
Fiber1={pixel1,pixel2,pixel3,pixel4,pixel5}
Fiber2={pixel1,pixel2,pixel3,pixel6,pixel7}
then whether the fiber1 and fiber1 have the same data structure as the above, or
Fiber1={pixel1,pixel2,pixel3,pixel4,pixel5}
Fiber2={pixel6,pixel7}
or maybe DTIStudio generates three fibers:
Fiber1={pixel1,pixel2,pixel3}
Fiber2={pixel6,pixel7}
Fiber3={pixel4,pixel5}
Is it possible that the last two cases happening?
2009-03-17，susumu <susumu at mri.jhu.edu> ：
>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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>
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