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

[susumu]

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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