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Subject:

Re: Help needed with Anatomy Toolbox

From:

"Simon B. Eickhoff" <[log in to unmask]>

Reply-To:

[log in to unmask]

Date:

Fri, 25 Jul 2008 09:51:09 +0200

Content-Type:

text/plain

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Parts/Attachments

text/plain (85 lines)

Dear Omer


> I'm running the application via the command-line (not within SPM). 

But you still have SPM in the MATLAB path, correct? The Anatomy Toolbox relies on some of the i/o functions of SPM and hence you need them to be accessible. Having said that, it's still a good idea to start SPM before you use any of the Toolbox scripts from the command line, as this ensures that all global variables are set correctly.


> I want to run the "batch" tool to identify multiple MNI coordinates.
> I prepared a text file containing my coordinates, organized thus:
> 10 10 10
> 20 20 20
> etc.

Just to make sure, these coordinates are mm, not voxel coordinates? If you supply voxel coordinates, you shouldn't get anything meaningful.



> When prompted to choose the _MPM.mat file to be used as map, I 
> select the AllAreas_v15_MPM.mat file that is located in the "Anatomy" directory. 
> Unless I'm wrong, this is the file to choose for whole brain labeling.

You are completely right. This is correct.


> Then, I choose my .txt file and click on the MNI option when asked, 

With this option you tell the program, which coordinate space (standard or anatomical MNI) the coordinates you provided in the textfile are in.


> I then get the following error message, and the window "freezes":
> 
> >> ??? Bad image handle dimensions.
> 
> Error in ==> se_TabList at 67
>    ProbMax(1:size(xyz,2),PM+1) =
> spm_sample_vol(MAP(PM).PMap,xyz(1,:),xyz(2,:),xyz(3,:),0)';

If the coordinates you privided are MNI mm-space, this message basically means, that SPM can't read (at least) one of the probability map files located at /Anatomy/PMaps. So you may want to check whether there has been a problem with unzipping by comparing the files sizes of the images. In addition to that, you might also want to test whether you can open the images using spm_display or by starting the Toolbox GUI and using the "Cytoarchitectonic probabilities at defined MNI coordinates" utility. 


Hope this helps
Simon




> 
> ??? Error using ==> se_TabList;
> Bad image handle dimensions.
> 
> ??? Error while evaluating uicontrol Callback
> 
> 
> Any ideas how to resolve this problem?
> 
> Thanks for your help!
> Omer
> 

-----------------------------------------
 
Simon Eickhoff
Institut for Medicine (IME);  Research Center Jülich
Leo-Brandt-Str. 5;  52425  Juelich, Germany
Phone + 49 2461-61-5219 / Fax + 49 2461-61-2820
e-mail: [log in to unmask]  /  [log in to unmask] 



-------------------------------------------------------------------
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Forschungszentrum Jülich GmbH
52425 Jülich

Sitz der Gesellschaft: Jülich
Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
Vorsitzende des Aufsichtsrats: MinDir'in Bärbel Brumme-Bothe
Geschäftsführung: Prof. Dr. Achim Bachem (Vorsitzender),
Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt,
Dr. Sebastian M. Schmidt
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