[Mristudio-users] Questions on the Functions of DTI Studio

[Luke Back]

Dear Prof. Hangyi Jiang

I deeply appreciate your dedicated answers for my rough questions. To be
honest, I somewhat understand your comments and paper. To comprehend your
paper,I come to realize that I need to study and review again various
backgrounds including linear algebra, vectors, NMR spectroscopy, fluid
mechanics, and so on. Although it is not easy for me to understand your
thesis paper fully, I will step by step build up my knowlege to comprehend
it. I believe that your paper is worthy of my study analyzing my data.

Dear Prof. Jiang, however, I also need the best settings to analyze my data
practically. I am very concernd about my request that I would like you to
set up the optimal settings applied to my MRI pictures since this request
seems to be ill-mannered as a scholar. Yet I am just a graduate student
who needs to learn a lot of things. To understand your paper, I attempt to
teach myself linear algebra, vectors, NMR spectroscpy, fulid mechanics, and
so on, but I conclude that I require more time studying these things.

This is the reason I sent  all my data to you. I wish I could meet you
person to person and learn from you, but I could not. So could you please
help me to find out best settings for my case?I would like you to see my
case and give me the information of the optimal settings. Hopefully,I might
want you not to get offended by my petition.

I would like to be an expert for DTI studio someday, and your help will be
the starting point.

Thank you.
Sincerely Luke.



 TueI , Sep 18, 2012 at 12:05 AM, Hangyi Jiang <hjiang at jhmi.edu> wrote:

> hello,
>
>
>
> Q1: I do not understand why I choose to “Create a mask…tab” and “the
> number should be 150."
>
> I do not understand this function either
>
>
> A: we are not interesting in the "tensor" in the background area, the
> "background noise level" threshold will mask out the background area of the
> image. only the area within the brain will be calculated.  you can decide
> this threshold by read out the image intensities in the background area
> (usually do this based on the B0 image).  or you can create a "binary mask
> image" based on an anatomy image. in this "binary mask", the background
> area or the area you are not interested in are given a value 0,  all others
> are given a non-zero values. the program can use this "binary mask" to do
> same thing as the "background noise level" threshold does.
>
> Q2: I do not understand functions in Method tab and in Verify the result
> tab.
> Should I check or change any of these to obtain the optimal resolution?
>
> A: "verify the result" is usually used for automatic outlier rejection
> method. for your case, you may not need them.
>
>
> Q3: I do not understand why I put” the number,150,"  in the Background
> noise level tap
>
> A: see the answer for Q1;
>
> Q4: I do not understand why I uncheck “Consider B-Value.”  I do not
> understand this function either
>
> A:  mathematically, B-value serves as a scaling factor for the results, if
> you are only interesting in the relative measurements (like FA map), don't
> worry about B-value. if you are interesting in absolute value of some
> measurement (like eigen values), B-value will scale down the read-out image
> intensities.  for detail, you may refer to the paper:
> Hangyi Jiang, Peter C.M. van Zijl, Jinsuh Kim, Godfrey D. Pearlson &
> Susumu Mori, "DtiStudio: Resource Program for Diffusion Tensor Computation
> and Fiber Bundle Tracking" Computer Methods and Programs in Biomedicine,
> vol. 81, pp106-116, 2006.
>
>
>
> : I do not understand why I put” the number,0.2,"  in the Start Tracking
> tap
>
>        I do not understand why I put” the number,0.2," and “the number,
> 60,”respectively  in the Stop  Tracking tap.
>
>        I do not understand these functions either
>
>
> A:  these values control how will you do fiber tracking (when to start,
> when to stop..), again, you can refer the paper I mentioned above.
>
> best,
>
> hangyi
>
>
> ________________________________
> From: Luke Back [lightgiving2004 at gmail.com]
> Sent: Monday, September 17, 2012 4:59 AM
> To: Hangyi Jiang; mristudio-users at mristudio.org
> Subject: Re: Questions on the Functions of DTI Studio
>
> Dear Prof, Hangyi Jiang and DTI experts
> I am very grateful to your keen interests in my case and thoughtful
> answers. It was very helpful to my problems.
> Actually, I have another question on DTI settings.
> For this, I am attaching several documents including 1) DICOM file that I
> have studies, 2) a gradient table applied to DICOM files, and 3) DTI
> settings to which I apply.
> I would like you to help to find out the settings of the optimal
> resolution for my case so I could see the the clearest pictures derived
> from MRI.
> A friend of mine (she) taught me several numbers and conditions applied to
> my case, but she and I do not know anout each meaning of the number and
> condition as to why these numbers and conditions should be inserted into.
> She said that she also barely comprehended when learning.
> I ask five questions in the "DTI Data Analysis (The Basic Settings)"
> document I am attaching
> Could you please help me out for this matter?
>
> Thank you so much.
> Sincerely Luke.
>
> On Wed, Sep 12, 2012 at 3:32 AM, Hangyi Jiang <hjiang at jhmi.edu<mailto:
> hjiang at jhmi.edu>> wrote:
> hello, Luke,
>
> I got your questions from forwarded message.
>
> the ROI tools in "fiber" tab is used for fiber selection, only select
> fibers will be displayed,  but not the ROIs
> the ROI tools in "ROI" tab is used for simple ROI creation, not for fiber
> selection.
>
> if you just need one ROI for fiber selection (suppose that you used "OR"
> operation), you may use "ROI save" button (of the "ROI operations" group of
> the "fiber" tab) same the ROI as a binary image, and load the save image
> file in (file_format = RAW, data_type = BYTE), and take a look about ROI.
>
> if you used multiple ROIs for for fiber selection (e.g. using OR-AND
> combination), the situation is very complicated. you may need to save them
> as "binary map" to get a series binary images for each of ROIs.
>
> about your 2nd question, you may use "# of voxels of fiber passing
> through" as the measurement of you wanted.
>
> best,
>
> hangyi
>
>
> ________________________________
> From: Luke Back [lightgiving2004 at gmail.com<mailto:
> lightgiving2004 at gmail.com>]
> Sent: Monday, September 10, 2012 11:24 PM
> To: Xin Li; mristudio-users at mristudio.org<mailto:
> mristudio-users at mristudio.org>
> Subject: Questions on the Functions of DTI Studio
>
> Hello, DTIstudio Experts
>
> I am using this program so as to obtain FA, RA, radial and axial
> diffusivities. To do so, I am using “ROI Drawing” function, attaining these
> parameters. Before that, I also primarily check my ROI (region of my
> interest) through “Fiber Tracking” function to determine which parts I am
> supposed to draw. It is because that the fiber tracking section also
> includes “ROI-Drawing Enable” function by which I could exactly see the
> anatomical parts I desire. For example, if my ROI is corpus callosum, I
> could see this part through the fiber tracking section.
>
> However, when I return to “ROI” section, I no more use this information. I
> mean I should turn off “ROI-Drawing Enable” function in “Fiber Tracking”
> section. I re-draw the target. Due to this process, I do not know where the
> fibers I desire pass through because “ROI Drawing-Operation“in “ROI”
> section does not support fiber tracking information. Could you guys please
> solve this matter?
>
> One more question is that I am wondering if I calculate fiber volume after
> I draw ROI by “ROI-Drawing Enable” function in “Fiber Tracking” section.
>
> Overall, I summarize my questions as follows:
> 1)     How can I sustain ROI drawing in “Fiber Tracking” section although
> I work in “ROI” section?
> 2)     Is there way to calculate fiber volume after I draw ROI by
> “ROI-Drawing Enable” function in “Fiber Tracking” section?
> p.s. I am attaching what I have done
>
>
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