How to bring the (non-struct array object) pixel data into the right format?

Question

Katharina Hecker 2018-6-16

0
链接

此问题的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/405922-how-to-bring-the-non-struct-array-object-pixel-data-into-the-right-format

评论： Katharina Hecker 2018-6-16

I am trying to bring an image volume (181x299x305 double (=FilteredVolume)) from Matlab to the 3D Slicer (with the MatlabBridge Extension). The size of the voxels are [0.0500 0.0500 0.0500]. The number of slides from which the volume was created are 181.

I have used the code:

load('matrixfilteredvolume.mat');
img.ijkToLpsTransform = [ 0.05 0 0 0; 0 0.05 0 0; 0 0 0.05 0; 0 0 0 1];
img.pixelData=FilteredVolume
cli_imagewrite(img.ijkToLpsTransform.FilteredVolume, img);

--------------------

But now I get the Error:

    img = 
    struct with fields:
    ijkToLpsTransform: [4×4 double]
            pixelData: [181×299×305 double]
    Struct contents reference from a non-struct array object.
    Error in (line 19)
    cli_imagewrite(img.ijkToLpsTransform.FilteredVolume, img);

Can anybody help me how I should change the structure contents of my matrix to make this code work?

I am working on it quit a long time, so I would be very pleased about any suggestions!

0 个评论
显示 -2更早的评论隐藏 -2更早的评论

请先登录，再进行评论。

请先登录，再回答此问题。

Answer 1

Walter Roberson 2018-6-16

0
链接

此回答的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/405922-how-to-bring-the-non-struct-array-object-pixel-data-into-the-right-format#answer_324906

在 MATLAB Online 中打开

You construct

img.ijkToLpsTransform = [ 0.05 0 0 0; 0 0.05 0 0; 0 0 0.05 0; 0 0 0 1]

so img.ijkToLpsTransform is a numeric vector.

But then you try

cli_imagewrite(img.ijkToLpsTransform.FilteredVolume, img);

implying that you think img.ijkToLpsTransform is a struct.

Perhaps you wanted

cli_imagewrite(img.FilteredVolume, img);

10 个评论
显示 8更早的评论隐藏 8更早的评论

Guillaume 2018-6-16

At this point, it's probably easier if you attach to your question the unmodified m file that you're supposed to edit.

Katharina Hecker 2018-6-16

matrixvolumeto3dslicer.m

ok, thanks a lot for your help!!!

请先登录，再进行评论。

Answer 2

Image Analyst 2018-6-16

0
链接

此回答的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/405922-how-to-bring-the-non-struct-array-object-pixel-data-into-the-right-format#answer_324913

在 MATLAB Online 中打开

Try this:

load('matrixfilteredvolume.mat');
% "img" has now been poofed into memory.
img.ijkToLpsTransform = [ 0.05 0 0 0; 0 0.05 0 0; 0 0 0.05 0; 0 0 0 1];
% Assign the pixelFata field to FilteredVolume.
% We KNOW that FilteredVolume already exists because you got past this line.
img.pixelData=FilteredVolume
% Now write out FilteredVolume:
cli_imagewrite(FilteredVolume, img);

I'm not really sure what your function cli_imagewrite() does since you didn't include it but presumably it wants something like FilteredVolume as the first argument and a structure as the second argument.

9 个评论
显示 7更早的评论隐藏 7更早的评论

Katharina Hecker 2018-6-16

编辑：Walter Roberson 2018-6-16

在 MATLAB Online 中打开

the m file is created from the 3D Slicer like I attached it above. The code which has to be changed accordingly to load matrices inside the Slicer is this one (raw type like in the file above):

img=cli_imageread(inputParams.inputvolume);
outputParams.min=min(min(min(img.pixelData)));
outputParams.max=max(max(max(img.pixelData)));
img.pixelData=(double(img.pixelData)>inputParams.threshold)*100;
cli_imagewrite(inputParams.outputvolume, img);

I tried to figure out how to change it to not create a module but to actually load data inside the slicer.

Therefore the first line is not needed

img=cli_imageread(inputParams.inputvolume);

the information which is needed is shown as followed:

load('matrixfilteredvolume.mat');
img.ijkToLpsTransform = [ 0.05 0 0 0; 0 0.05 0 0; 0 0 0.05 0; 0 0 0 1];
img.pixelData=FilteredVolume

and the function:

cli_imagewrite(inputParams.outputvolume, img);

which has to adjusted according to my data,

Unfortunately that is all I know.

As I said: I could not find the correct inputParams or rather had too less input arguments...

Thanks for your help and understanding!

Katharina Hecker 2018-6-16

编辑：Image Analyst 2018-6-16

在 MATLAB Online 中打开

The m file which I attached is created by the software '3D Slicer'by using the Module 'Matlab Module Generator' so I can't see how the m file which I attached is created.

I just have an additional .bat file, which is also created automatically with the 'Matlab Module Generator', and an xml file, which contains after creation this information:

<?xml version="1.0" encoding="utf-8"?>
<executable>
  <category>Matlab</category>
  <title>matrixvolumeto3dslicer</title>
  <description><![CDATA[Perform a simple image processing and image statistics computation in Matlab.]]></description>
  <version>0.0.0.1</version>
  <documentation-url>http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/MatlabBridge</documentation-url>
  <license/>
  <contributor>Andras Lasso (PerkLab)</contributor>
  <acknowledgements><![CDATA[SparKit is a project funded by Cancer Care Ontarioand the Ontario Consortium for Adaptive Interventions in Radiation Oncology (OCAIRO) to provide free, open-source toolset for radiotherapy and related image-guided interventions.]]></acknowledgements>
  <parameters>
    <label>Processing Parameters</label>
    <description><![CDATA[Parameters for the processing]]></description>
    <integer>
      <label>Threshold</label>
      <description><![CDATA[All voxels below this value will be set to zero]]></description>
      <longflag>threshold</longflag>
      <default>50</default>
      <constraints>
        <minimum>-2000</minimum>
        <maximum>5000</maximum>
        <step>5</step>
      </constraints>      
    </integer>
  </parameters>
  <parameters>
    <label>IO</label>
    <description><![CDATA[Input/output parameters]]></description>
    <image>
      <label>Input Volume</label>
      <description><![CDATA[Input volume to be filtered]]></description>
      <longflag>inputvolume</longflag>
      <channel>input</channel>
    </image>
    <image>
      <label>Output Volume</label>
      <description><![CDATA[Output filtered]]></description>
      <longflag>outputvolume</longflag>
      <channel>output</channel>
    </image>
  </parameters>
  <parameters>
    <label>Output</label>
    <description>Matlab command output</description>
    <double>
      <label>Minimum</label>
      <description><![CDATA[Image mininum]]></description>
      <name>min</name>
      <channel>output</channel>
      <default></default>
    </double>    
    <double>
      <label>Maximum</label>
      <description><![CDATA[Image maximum]]></description>
      <name>max</name>
      <channel>output</channel>
      <default></default>
    </double>    
  </parameters>
</executable>
---------

In the m file there are these lines which have to be adjusted according to your data, to import data or to generate a module which process data inside the slicer. These lines are the following:

function outputParams=newforima(inputParams)
img=cli_imageread(inputParams.inputvolume);
outputParams.min=min(min(min(img.pixelData)));
outputParams.max=max(max(max(img.pixelData)));
img.pixelData=(double(img.pixelData)>inputParams.threshold)*100;
cli_imagewrite(inputParams.outputvolume, img);