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

Thu Mar 19 05:59:46 EDT 2009

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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