[Mristudio-users] how to save the transformation matrix from alandmarker based transformation

[susumu mori]

Hi Yi,

Currently we don't have a program for what you need. We use our own codes in
IDL or SPM (MatLab). Ken and Andreia are doing it routinely. Please ask them
if you have specific questions. There are a couple of points I want to make;

1) If you normalize your data to an atlas, all your data will have similar
shape. Then, you can perform pixel-by-pixel statistics. This is voxel-based
analysis. I believe SPM has an array of tools for this.

2) If you transform an atlas (especially our white matter parcellation map
(WMPM)) to the shape of your data, you will get numbers (such as volume, FA,
MD, etc) from 100-176 regions of each brain (automated segmentation). This
process converts image data to a string of numbers. Then the data can be
analyzed by Excel for statistical analyses.

The approach #1 is ideal for strong abnorality in a small region. The
approach can theoretically detect abnormality as small as one pixel but each
pixel has low statistical power.

The approach #2 is ideal for diffuse abnormality. It groups all pixels that
belong to one of the 100-176 regions, which increases the statistical power
but if the abnormal region is only a small portion of one segment, the pixel
grouping reduces the sensitivity.

So, the two approaches are complementary. We have been working on a
statistical tool for approach #1 but it'll take some time.

Susumu

On Thu, Aug 6, 2009 at 2:32 PM, Yi Jiang <yj3 at duke.edu> wrote:

>  Hi Dr Mori,
>
> Thank you very much. Andreia and Xin have helped me to make it work.
>
> I have another question. I am wondering if you have suggestion or software
> about averaging eigenvectors or tensors. In other words, if we have, say,
> DTI dataset of 10 brains, all registered together, how can we calculate the
> mean (and variation) of the 10 primary eigenvector field or calculate the
> mean (and variation) of the 10 tensor field?
>
> Any suggestion is highly appreciated!
>
> Yi
>
>
> ----- Original Message -----
> *From:* susumu mori <susumu at mri.jhu.edu>
> *To:* Yi Jiang <yj3 at duke.edu> ; DTI Studio, ROI Editor, Landmarker
> Questions/Support <mristudio-users at mristudio.org> ; Xin Li<xli16 at jhmi.edu>; ANDREIA
> FARIA <afaria1 at jhmi.edu>
> *Sent:* Tuesday, August 04, 2009 9:59 PM
> *Subject:* Re: [Mristudio-users] how to save the transformation matrix
> from alandmarker based transformation
>
> Hi Yi,
>
> I believe you can save the matrix. Xin should know how to do it.
> As for the matrix combination, I remember that we discussed about exactly
> the same topic in my lab. I thought that answer was Yes, but don't exactly
> remember how to do it. Andreia and Xin, do you know how to do it?
>
> On Tue, Aug 4, 2009 at 4:31 PM, Yi Jiang <yj3 at duke.edu> wrote:
>
>>  Dear All,
>>
>> I have tried to look through the online manual, but could not find the
>> answer.
>>
>> I tried to use the landmark based transformation (translation) from the
>> main menu of the Landmarker window. The result is pretty good. However, I do
>> not know how to save the transformation matrix. I tried to click the "save
>> transformation matrix" button in the subject window. It seems two files was
>> saved (.hdr? and .dat), but the file sizes were very small.
>>
>> I also want to combine the transformation matrix from the landmark based
>> translation with a AIR linear rigid, a AIR linear affine transformation, and
>> a LDDMM matrix. Can I do that? I do not know if the transformation matrix
>> from landmark based translation is a AIR format, or LDDMM raw format, or a
>> LDDMM vtk format, which was asked in the combine matrix window.
>>
>> The last question may be stupid: if there are defined landmarks in the
>> memory, when I click on AIR linear or multichannel LDDMM (not from the main
>> menu, but the buttons in the subject window), those landmarks were not used
>> in transformation, right?
>>
>> Thank you very much!
>>
>> Best,
>> Yi
>>
>>
>>
>>
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