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Mia 2.5

version 1.4 (345 KB) by

Medical Image Analysis GUI.

4.06667
15 Ratings

33 Downloads

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mia - medical image analysis
This Matlab GUI enables you to do analysis on medical images. A collection of tools are provided to perform slice or volume based analysis. On the other hand the program can be considered as a wrapper of useful previously developed and own matlab tools for medical image processing. The following new features are included in the latest version:

For more information about the all included options of mia find the "miahistory.doc" file at
http://petunia.atomki.hu/~balkay/mia/miahistory.doc

Installing, running: unzip the downloaded file, you will have a mia directory containing the whole utility. Add the mia directory (and ALL subfolders) to your matlab path. Run the mia function.
Before installation delete the previous version of MIA if exists.

Comments and Ratings (48)

Zhouping wei

I mean 32644-loadminc is not going to work in mia 2.5

Zhouping wei

To Laszolo: loadminc.m at "http://www.mathworks.com/matlabcentral/fileexchange/32644-loadminc" cannot be included in mia 2.5 @ "...mia/Tools" folder

Laszlo Balkay

Laszlo Balkay (view profile)

Comment to Zhouping wei:
it would be better to send me your specific image file you would like to read (to balkay@pet.dote.hu). Using a minc file, I suggest to update the loadminc.m file in the ...mia/Tools folder with
http://www.mathworks.com/matlabcentral/fileexchange/32644-loadminc
  

Zhouping wei

To Laszolo: the image readers with mia 2.5 has lots of problems, would you please provide some testing images. I'm running on matlab R2014b

Zhouping wei

when reading minc file, an error message as follows occurred:
Undefined function or variable "precision_range".

Error in loadminc (line 102)
volume_ = zeros(dimlenx,dimleny,dimlenz,precision_range);

Laszlo Balkay

Laszlo Balkay (view profile)

I updated for MATLAB 2014b during the last upload.

AZama

AZama (view profile)

can this work on R2014a ?

syed

syed (view profile)

I had a dicom file in the diirector from which I ran mia but still get error

keerthana

Hey, I am facing the same problem as
Attempt to reference field of non-structure array.

Error in mia_3dcursor_gui>SliceModebutton_Callback (line 185)
mia_mainfigure_handles = guidata(handles.mia_mainfigure);

Error in gui_mainfcn (line 96)
        feval(varargin{:});

Error in mia_3dcursor_gui (line 42)
    gui_mainfcn(gui_State, varargin{:});
 
Error while evaluating uicontrol Callback

Kushagra

Hey, I am facing the same problem as H Amiri.

??? Error using ==> miinquire at 142
Error getting image dimensions from file A:\DATA\MATLAB\Documents/demofdgbrain.mnc

Error in ==> openimage at 173
DimSizes = miinquire (filename, 'imagesize');

I get this error when I try to open any .mnc file. I am also using MATLAB 200a and EMMA v1.0.0. If anyone has some idea about it please help. Also if someone knows about a working EMMA for windows that would be very helpful.

Thanks in advance. :)

H Amiri

Hi,
I got the following error while trying to read a .mnc file:

??? Error using ==> miinquire at 142
Error getting image dimensions from file ...\mia24\t3.mnc

I'm using MATLAB 2010a, and EMMA v0.9.8.
Anyone knows how to solve this error?

Thanks in advance

Hi ,is there a manual or easy way to learn how to use this programme.Anyone who managed to use it could please inform me how he did it .Moreover I use Matlab R2010a and i can not open any file,is there something i must do in order to open a dicom image ?I get this error also :

??? Attempt to execute SCRIPT uigetfiles as a function:
C:\Users\User1\Documents\MATLAB\matlab DWI\TEST\Mia24\uigetfiles.m

Error in ==> mia_gui>OpenImageFilemenuItem_Callback at 197
                [FilesSelected, dir_path] = uigetfiles(...

Error in ==> gui_mainfcn at 96
        feval(varargin{:});

Error in ==> mia_gui at 43
    gui_mainfcn(gui_State, varargin{:});
 
??? Error while evaluating uimenu Callback

 thanks in advance

Laszlo Balkay

Laszlo Balkay (view profile)

Comment to Edwin:

The uigetfiles.m is actually a binary file which is compiled with an old environment. The current uploaded version (2.4) works with the Matlab version up to 2010ab. I plan to upgrade the code soon.

Laszlo

Edwin

Edwin (view profile)

sorry for forgetting to post the error msg,

 
??? Attempt to execute SCRIPT uigetfiles as a function:
D:\UM_MASTER\Greta\matlab\mia24\ToolsFromOthers\uigetfiles.m

Error in ==> mia_gui>OpenImageFilemenuItem_Callback at 197
                [FilesSelected, dir_path] = uigetfiles(...

Error in ==> gui_mainfcn at 96
        feval(varargin{:});

Error in ==> mia_gui at 43
    gui_mainfcn(gui_State, varargin{:});
 
??? Error while evaluating uimenu Callback

Edwin

Edwin (view profile)

Hi, I have set the path as the introduction said, but errors still come out like below when i click on the "open first image meun", any one knows how to solve it?

Thanks a lot lot lot

Vino

Vino (view profile)

Hi Laszlo,
   I have some problem in opening the DICOM images or DICOMDIR....I am getting the following error

Error using ==> images\private\dicom_set_mmeta_encoding. Invalid transfer syntax UID "1.2.840.10008.1.2.4.91"

What this error mean..? can u plz help...
Thanks a lot

Laszlo Balkay

Laszlo Balkay (view profile)

I have corrected the link of the documentation

The documentation is not available please put the documentation online thanks!!! i need some information about sliceomatic, 3dcursor and 3d reconstruction of mri thanks!

Silvina

Hi Laszlo,
I have the same problem that Yawar mentioned previously. Is there a way to read minc files without the EMMA package?
Thanks a lot!

Jin

Jin (view profile)

good work!

Laszlo Balkay

Laszlo Balkay (view profile)

Comment to Yawar Rehman:
Sorry, I was just reading your questions.
I wrote a new function to read the mnc format files based on the NETCDF bultin matlab library. If you intrested in I will send you (balkay@pet.dote.hu)

Yawar Rehman

gr8 work ... can u tell me that from where can i get emma package to dl ... the error occurs when i select a .mnc format file.
can u plz help
"MEX-files with .dll extensions will not execute in a future version of MATLAB.
For reading minc file you should install the EMMA package from MNI."

Good work!

Preeti

Preeti (view profile)

please give some examples.

Laszlo Balkay

Laszlo Balkay (view profile)

Comment to Kiran:
I never try 3D US data. Is this a dicom format?

Kiran

Kiran (view profile)

Hi

Whether this tool will read the Ultrasound raw image data
and is it possible to rotate the 3D data////

ucd puri

woooo, awsome, thats very good, thank you ver much...

Trevor Cooper

- Open the MATLAB built-in documentation (type doc at the >> prompt, select "Product Help" from the "Help" menu or press F1). Depending on your platform one/all will work.
- Display the Help Navigator in the Help window by selecting "Help Navigator" from the "View" menu if it isn't already visible on the left of the Help window.
- Select the "Contents" tab in the Help Navigator if it's not already selected.
- Expand the "MATLAB" node.
- Expand the "Desktop Tools and Development Environment" node.
- Expand the "Workspace, Search Path, and File Operations" node.
- Expand the "Search Path" node.
- Select the "Viewing and Setting the Search Path" node.
- Everything you need to know is there in great detail.

Good luck.

ucd puri

Hi , I am not an expert in matlab, just learning how to make a Matlab based image analysis GUI for my work. I dont know how to do the following step. please help Regards n thanks Tanuj
Add the mia directory (and ALL subfolders) to your matlab path

Laszlo Balkay

Comment to Nam-Beom Kim: The *.img file should be an analyse formatted image file. Do you have *.hdr also next to the *.img file? Another reason would be: the lower-upper case extension is not identical for mia (*.IMG might be wrong). If you could not fix the problem, please send me your files via email (my email server accepts files up to 15Mb)

I hope this help,

Laszlo

Nam-Beom Kim

when i was trying to open '*.img', error message shows me like this; " No image file was selected. The supported files are:
*.img;*.mnc;*.ima;*.cub;*.mat; " i tried to severals times with different file formats, But the result was always same. what did i do wrong?

Laszlo Balkay

Comments to Asif Rizwan: I think you did not add the "mia directory" (and ALL SUBFOLDER) to your matlab path (same problem as with Suneel Battula). See the Description of Mia. Copying the "mia dir" to your "matlab work" dir is NOT ENOUGH.

Asif Rizwan

Hi, I am also facing the same problem as Suneel Battula. I copied the mia dir in the work file. It gives error messages. Where should I copy the dcm files?

Laszlo Balkay

Comments to Suneel Battula: I think you did not add the "mia directory" (and ALL subfolders) to your matlab path. See the Description of Mia.

Suneel Battula

Hi

The tool looks great but i havent been able to analyze it. when i try opening DICOM files it gives me the following error...could you let me know if I have to make any changes to the code?

Thanks

??? Undefined function or method 'uigetfiles' for input arguments of type 'char'.

Error in ==> mia_gui>OpenImageFilemenuItem_Callback at 197
                [FilesSelected, dir_path] = uigetfiles(...

Error in ==> gui_mainfcn at 95
        feval(varargin{:});

Error in ==> mia_gui at 43
    gui_mainfcn(gui_State, varargin{:});

??? Error using ==> mia_gui('OpenImageFilemenuItem_Callback',gcbo,[],guidata(gcbo))
Undefined function or method 'uigetfiles' for input arguments of type 'char'.

??? Error while evaluating uimenu Callback

??? Undefined function or variable 'loaddcmdir'.

Error in ==> mia_gui>OpenDICOMDIRfromNew_Callback at 453
[dcmSeries, dcmPatient, SeriesList, SeriesListNumInfo] = loaddcmdir;

Error in ==> gui_mainfcn at 95
        feval(varargin{:});

Error in ==> mia_gui at 43
    gui_mainfcn(gui_State, varargin{:});

??? Error using ==> mia_gui('OpenDICOMDIRfromNew_Callback',gcbo,[],guidata(gcbo))
Undefined function or variable 'loaddcmdir'.

??? Error while evaluating uimenu Callback

malikireddy krishnareddy

thanks Lazlo ..

Laszlo Balkay

Comments to Torsten Ruest:
Hi,

opening error: I think there would be problem about the file format. To see more details you should send me your analyse format images to balkay@pet.dote.hu (the attached file can be up to 30Mb)

Overlying images: principally there is possibility to overly images with mia, but I did not check it at any situation. Please send me your MRI image, also.

I hope this help,

Laszlo
  

Torsten Ruest

Hi,
when I try to open an ANALYZE image, the Matlab command window displays the following:
 
Warning: slider control requires that Min be less than Max
Control will not be rendered until all of its parameter values are valid.

Another little window opens with the followong message:

Unknown Data Type (Precision?)

Another question: I have FSL stats output images (one negative, the other positive) and would like to overlay them on an anatomical image to get a continous color bar of the significant voxels. Is this possible?

Cheers,

Laszlo Balkay

Comments to Malikireddy Krishnareddy: I think you did not add the "mia directory" (and ALL subfolders) to your matlab path. See the description above.

malikireddy krishnareddy

??? Undefined function or method 'uigetfiles' for input arguments of type 'char'.

Error in ==> mia_gui>OpenImageFilemenuItem_Callback at 197
                [FilesSelected, dir_path] = uigetfiles(...

Error in ==> gui_mainfcn at 75
        feval(varargin{:});

Error in ==> mia_gui at 43
    gui_mainfcn(gui_State, varargin{:});

??? Error using ==> mia_gui('OpenImageFilemenuItem_Callback',gcbo,[],guidata(gcbo))
Undefined function or method 'uigetfiles' for input arguments of type 'char'.

??? Error while evaluating uimenu Callback

I get this error , what do i do to run ?
It is encouraging once it starts going , i can test it with MRI images , angio , with pics from Doctors with me.
I will definitely give a feed back and analysis report of certain thigns, with inputs from doctors , if something needs to be further developed or required for is. Please help me with this error , or what iam i doing wrong, iam trying to access the file from menu, but then i get this error
Regards
Krishna

Jackson Shen

Excellent tools

DERRAZ Foued

it can be developed to support others alalysis process

Shuhai Chen

I don't know how to run. please give some examples

Shoan Kale

This is an excellent program in terms of functionality. Some complaints: cannot save as a MINC file while all other formats are no problem; ROI stat functions and 3D cursor are not stable. Very good piece of software otherwise.

Lars Ewell

Seems OK. However, our version (6.5) of Matlab (released 6/18/02) apparently has an old version of the 'Toolbox' that is incompatible with this. This fact, unfortunately, required me to downgrade my rating.

Adam Marcotte

Has some great features, but also has some bugs, implementation issues and interface deficiencies. None of the text in the slice-o-matic tool displays correctly. Needs a custom-resize function or turn resize off.

Andres Jimenez Guerra

Havent uised it yet, but it will help me a lot for my undergraduate thesis. Medical Physics

luciano marchionno

Updates

1.4

The tool was updated for MATLAB 2014b.

1.2

License info

1.1

License info

Uploading Version 2.3

Uploading screenshot.

The description was not correct.

MATLAB Release
MATLAB 7.13 (R2011b)
Acknowledgements

Inspired by: Sliceomatic

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