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

[Javier Navas]

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



Could you explain me why the FA mean values are different?
THANK YOU

Javier

2009/3/14 susumu <susumu at mri.jhu.edu>

>  Hi Javier,
>
>
>
> I'm not sure if I'm answering your question, but here I listed what you can
> do after you get a tractgraphy result;
>
>
>
> 1) Click the "statistics" button and specify an MRI image (e.g. FA map) you
> want to quantify. This gives you the average and standard deviation of all
> pixels included in the tract (this is not what you want).
>
> 2) Then click "profile" button. This give you pixel values within each
> slice in axial, coronal, and sagittal orientations. This works nicely if the
> tract of your interest has a linear shape. For tracts like the corpus
> callosum (U-shape), this approach has some issue.
>
> 3) Save the tract as a binary image (1/0 map). Load this binary image as an
> image to RoiEditor as well as a map you want to quantify (e.g. FA map).
> Using the binary image and the thresholding tool, define an object that
> identify pixels with value "1"; namely, redefine the tract as an object.
> Bring the FA map as an active image and right-click the object you defined
> in the "object list". This allows export (text file) of FA values of all
> pixels that belong to the tract you defined. You can read this text file
> into Excel and create a histogram
>
> 4) You can normalize the binary image to one of the atlas provided in
> Landmarker. By normalize population data, you can create probabilistic tract
> maps. Using RoiEditor, you can mask FA maps by tractography results and then
> normalize. This may allow you to do pixel-based analysis in an atlas space.
> After normalization, you can also "segment" the tracking result into the
> corpus callosum region and corona radiata region by combining your binary
> tracking image and "white matter parcellation map (WMPM)" provided in
> RoiEditor.
>
>
>
> I must admit that currently manuals of RoiEditor and Landmarker are very
> limited. We are working on it and it may take some time. If you think one of
> the above 4 methods can provide what you want, you can contact us for more
> specific instruction.
>
>
>
> Susumu
>
>
>  ------------------------------
>
> *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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